commit/galaxy-central: 2 new changesets

27 Aug 2012

2 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/f6d9557b6d77/
changeset:   f6d9557b6d77
user:        Tomithy
date:        2012-08-26 12:22:23
summary:     re-integrated phyloviz to a new fork of galaxy-central with a =
tat of minor touch up; save and edit now works
affected #:  19 files

diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/datatypes/data.py

--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -719,7 +719,49 @@
     pass
=20
 class Newick( Text ):
-    pass
+    """New Hampshire/Newick Format"""
+    file_ext =3D "nhx"
+
+    MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu=
mns", readonly=3DTrue )
+
+    def __init__(self, **kwd):
+        """Initialize foobar datatype"""
+        Text.__init__(self, **kwd)
+
+    def init_meta( self, dataset, copy_from=3DNone ):
+        Text.init_meta( self, dataset, copy_from=3Dcopy_from )
+
+
+    def sniff( self, filename ):
+        """ Returning false as the newick format is too general and cannot=
 be sniffed."""
+        return False
+
+
+class Nexus( Text ):
+    """Nexus format as used By Paup, Mr Bayes, etc"""
+    file_ext =3D "nex"
+
+    MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu=
mns", readonly=3DTrue )
+
+    def __init__(self, **kwd):
+        """Initialize foobar datatype"""
+        Text.__init__(self, **kwd)
+
+    def init_meta( self, dataset, copy_from=3DNone ):
+        Text.init_meta( self, dataset, copy_from=3Dcopy_from )
+
+
+    def sniff( self, filename ):
+        """All Nexus Files Simply puts a '#NEXUS' in its first line"""
+        f =3D open(filename, "r")
+        firstline =3D f.readline().upper()
+        f.close()
+
+        if "#NEXUS" in firstline:
+            return True
+        else:
+            return False
+
=20
 # ------------- Utility methods --------------
=20


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/datatypes/xml.py
--- a/lib/galaxy/datatypes/xml.py
+++ b/lib/galaxy/datatypes/xml.py
@@ -76,3 +76,24 @@
             dataset.blurb =3D 'file purged from disk'
     def sniff( self, filename ):
         return False
+
+class Phyloxml( GenericXml ):
+    """Format for defining phyloxml data http://www.phyloxml.org/"""
+    file_ext =3D "phyloxml"
+    def set_peek( self, dataset, is_multi_byte=3DFalse ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek =3D data.get_file_peek( dataset.file_name, is_mul=
ti_byte=3Dis_multi_byte )
+            dataset.blurb =3D 'Phyloxml data'
+        else:
+            dataset.peek =3D 'file does not exist'
+            dataset.blurb =3D 'file purged from disk'
+
+    def sniff( self, filename ):
+        """"Checking for keyword - 'phyloxml' always in lowercase in the f=
irst few lines"""
+        f =3D open(filename, "r")
+        firstlines =3D "".join(f.readlines(5))
+        f.close()
+        if "phyloxml" in firstlines:
+            return True
+        return False
\ No newline at end of file


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/visualization/phyloviz/__init__.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/__init__.py
@@ -0,0 +1,1 @@
+__author__ =3D 'Tomithy'


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/visualization/phyloviz/baseparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/baseparser.py
@@ -0,0 +1,125 @@
+import json
+
+class Node(object):
+    """Node class of PhyloTree, which represents a CLAUDE in a phylogeneti=
c tree"""
+    def __init__(self, nodeName, **kwargs):
+        """Creates a node and adds in the typical annotations"""
+        self.name, self.id =3D nodeName, kwargs.get("id", 0)
+        self.depth =3D kwargs.get("depth", 0)
+        self.children =3D []
+
+        self.isInternal =3D kwargs.get("isInternal", 0)
+        self.length, self.bootstrap =3D kwargs.get("length", 0), kwargs.ge=
t("bootstrap", None)
+        self.events =3D kwargs.get("events", "")
+
+        # clean up boot strap values
+        if self.bootstrap =3D=3D -1:
+            self.bootstrap =3D None
+
+    def addChildNode(self, child):
+        """Adds a child node to the current node"""
+        if isinstance(child, Node):
+            self.children.append(child)
+        else:
+            self.children +=3D child
+
+
+    def __str__(self):
+        return self.name + " id:" + str(self.id) + ", depth: " + str(self.=
depth)
+
+
+    def toJson(self):
+        """Converts the data in the node to a dict representation of json"=
""
+        thisJson =3D {
+            "name"      : self.name,
+            "id"        : self.id,
+            "depth"     : self.depth,
+            "dist"      : self.length
+        }
+        thisJson =3D self.addChildrenToJson(thisJson)
+        thisJson =3D self.addMiscToJson(thisJson)
+        return thisJson
+
+    def addChildrenToJson(self, jsonDict):
+        """Needs a special method to addChildren, such that the key does n=
ot appear in the Jsondict when the children is empty
+        this requirement is due to the layout algorithm used by d3 layout =
for hiding subtree """
+        if len(self.children) > 0:
+            children =3D [ node.toJson() for node in self.children]
+            jsonDict["children"] =3D children
+        return jsonDict
+
+
+    def addMiscToJson(self, jsonDict):
+        """Adds other misc attributes to json if they are present"""
+        if not self.events =3D=3D "":
+            jsonDict["events"] =3D self.events
+        if not self.bootstrap =3D=3D None:
+            jsonDict["bootstrap"] =3D self.bootstrap
+        return jsonDict
+
+
+
+class PhyloTree(object):
+    """Standardized python based class to represent the phylogenetic tree =
parsed from different
+    phylogenetic file formats."""
+
+    def __init__(self):
+        self.root, self.rootAttr =3D None, {}
+        self.nodes =3D {}
+        self.title =3D None
+        self.id =3D 1
+
+    def addAttributesToRoot(self, attrDict):
+        """Adds attributes to root, but first we put it in a temp store an=
d bind it with root when .toJson is called"""
+        for key, value in attrDict.items():
+            self.rootAttr[key] =3D value
+
+    def makeNode(self, nodeName, **kwargs):
+        """Called to make a node within PhyloTree, arbitrary kwargs can be=
 passed to annotate nodes
+        Tracks the number of nodes via internally incremented id"""
+        kwargs["id"] =3D self.id
+        self.id +=3D 1
+        return Node(nodeName, **kwargs)
+
+    def addRoot(self, root):
+        """Creates a root for phyloTree"""
+        assert isinstance(root, Node)
+        root.parent =3D None
+        self.root =3D root
+
+    def generateJsonableDict(self):
+        """Changes itself into a dictonary by recurssively calling the toj=
son on all its nodes. Think of it
+        as a dict in an array of dict in an array of dict and so on..."""
+        jsonTree =3D ""
+        if self.root:
+            assert isinstance(self.root, Node)
+            jsonTree =3D self.root.toJson()
+            for key, value in self.rootAttr.items():
+                # transfer temporary stored attr to root
+                jsonTree[key] =3D value
+        else:
+            raise Exception("Root is not assigned!")
+        return jsonTree
+
+
+
+class Base_Parser(object):
+    """Base parsers contain all the methods to handle phylogeny tree creat=
ion and
+    converting the data to json that all parsers should have"""
+
+    def __init__(self):
+        self.phyloTrees =3D []
+
+    def parseFile(self, filePath):
+        """Base method that all phylogeny file parser should have"""
+        raise Exception("Base method for phylogeny file parsers is not imp=
lemented")
+
+    def toJson(self, jsonDict):
+        """Convenience method to get a json string from a python json dict=
"""
+        return json.dumps(jsonDict)
+
+    def _writeJsonToFile(self, filepath, json):
+        """Writes the file out to the system"""
+        f =3D open(filepath, "w")
+        f.writelines(json)
+        f.close()


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/visualization/phyloviz/newickparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/newickparser.py
@@ -0,0 +1,185 @@
+from baseparser import Base_Parser, PhyloTree
+import re
+
+class Newick_Parser(Base_Parser):
+    """For parsing trees stored in the newick format (.nhx)
+    It is necessarily more complex because this parser is later extended b=
y Nexus for parsing newick as well.."""
+
+
+    def __init__(self):
+        super(Newick_Parser, self).__init__()
+
+
+    def parseFile(self, filePath):
+        """Parses a newick file to obtain the string inside. Returns: json=
ableDict"""
+        with open(filePath, "r") as newickFile:
+            newickString =3D newickFile.read()
+            newickString =3D newickString.replace("\n", "").replace("\r", =
"")
+            return [self.parseData(newickString)], "Success"
+
+
+    def parseData(self, newickString):
+        """To be called on a newickString directly to parse it. Returns: j=
sonableDict"""
+        return self._parseNewickToJson(newickString)
+
+
+    def _parseNewickToJson(self, newickString, treeName=3DNone, nameMap=3D=
None):
+        """parses a newick representation of a tree into a PhyloTree data =
structure,
+        which can be easily converted to json"""
+        self.phyloTree =3D PhyloTree()
+        newickString =3D self.cleanNewickString(newickString)
+        if nameMap:
+            newickString =3D self._mapName(newickString, nameMap)
+
+        self.phyloTree.root =3D self.parseNode(newickString, 0)
+        if nameMap:
+            self.phyloTree.addAttributesToRoot({"treeName": treeName})
+
+        return self.phyloTree.generateJsonableDict()
+
+
+    def cleanNewickString(self, rawNewick):
+        """removing semi colon, and illegal json characters (\,',") and wh=
ite spaces"""
+        return re.sub(r'\s|;|\"|\'|\\', '', rawNewick)
+
+
+    def _makeNodesFromString(self, string, depth):
+        """elements separated by comma could be empty"""
+
+        if string.find("(") !=3D -1:
+            raise Exception("Tree is not well form, location: " + string)
+
+        childrenString =3D string.split(",")
+        childrenNodes =3D []
+
+        for childString in childrenString:
+            if len(childString) =3D=3D 0:
+                continue
+            nodeInfo =3D childString.split(":")
+            name, length, bootstrap =3D "", None, -1
+            if len(nodeInfo) =3D=3D 2: # has length info
+                length =3D nodeInfo[1]
+                # checking for bootstap values
+                name =3D nodeInfo[0]
+                try:    # Nexus may bootstrap in names position
+                    name =3D float(name)
+                    if 0<=3D name <=3D 1:
+                        bootstrap =3D name
+                    elif 1 <=3D name <=3D 100:
+                        bootstrap =3D name / 100
+                    name =3D ""
+                except ValueError:
+                    name =3D nodeInfo[0]
+            else:
+                name =3D nodeInfo[0]      # string only contains name
+            node =3D self.phyloTree.makeNode(name, length=3Dlength, depth=
=3Ddepth, bootstrap=3D bootstrap)
+            childrenNodes +=3D [node]
+        return childrenNodes
+
+
+
+    def _mapName(self, newickString, nameMap):
+        """
+        Necessary to replace names of terms inside nexus representation
+        Also, its here because Mailaud's doesnt deal with id_strings outsi=
de of quotes(" ")
+        """
+        newString =3D ""
+        start =3D 0
+        end =3D 0
+
+        for i in xrange(len(newickString)):
+            if newickString[i] =3D=3D "(" or newickString[i] =3D=3D ",":
+                if re.match(r"[,(]", newickString[i+1:]):
+                    continue
+                else:
+                    end =3D i + 1
+                    # i now refers to the starting position of the term to=
 be replaced,
+                    # we will next find j which is the ending pos of the t=
erm
+                    for j in xrange(i+1, len(newickString)):
+                        enclosingSymbol =3D newickString[j]   # the immedi=
ate symbol after a common or left bracket which denotes the end of a term
+                        if  enclosingSymbol =3D=3D ")" or enclosingSymbol =
=3D=3D ":" or enclosingSymbol =3D=3D ",":
+                            termToReplace =3D  newickString[end:j]
+
+                            newString +=3D newickString[start : end] +  na=
meMap[termToReplace] #+ "'"  "'" +
+                            start =3D j
+                            break
+
+        newString +=3D newickString[start:]
+        return newString
+
+
+    def parseNode(self, string, depth):
+        """ Recursive method for parsing newick string, works by stripping=
 down the string into substring
+        of newick contained with brackers, which is used to call itself.
+            Eg ... ( A, B, (D, E)C, F, G ) ...
+        We will make the preceeding nodes first A, B, then the internal no=
de C, its children D, E,
+        and finally the succeeding nodes F, G"""
+
+        # Base case where there is only an empty string
+        if string =3D=3D "":
+            return
+            # Base case there its only an internal claude
+        if string.find("(") =3D=3D -1:
+            return self._makeNodesFromString(string, depth)
+
+        nodes, children =3D [], []      # nodes refer to the nodes on this=
 level, children refers to the child of the
+        start =3D 0
+        lenOfPreceedingInternalNodeString =3D 0
+        bracketStack =3D []
+
+        for j in xrange(len(string)):
+            if string[j] =3D=3D "(":    #finding the positions of all the =
open brackets
+                bracketStack.append(j)
+                continue
+            if string[j] =3D=3D ")":    #finding the positions of all the =
closed brackets to extract claude
+                i =3D bracketStack.pop()
+
+                if len(bracketStack) =3D=3D 0:  # is child of current node
+
+                    InternalNode =3D None
+
+                    #First flat call to make nodes of the same depth but f=
rom the preceeding string.
+                    startSubstring =3D string[start + lenOfPreceedingInter=
nalNodeString: i]
+                    preceedingNodes =3D  self._makeNodesFromString(startSu=
bstring, depth)
+                    nodes +=3D preceedingNodes
+
+                    # Then We will try to see if the substring has any int=
ernal nodes first, make it then make nodes preceeding it and succeeding it.
+                    if j + 1 < len(string):
+                        stringRightOfBracket =3D string[j+1:]      # Eg. '=
(b:0.4,a:0.3)c:0.3, stringRightOfBracket =3D c:0.3
+                        match =3D re.search(r"[\)\,\(]", stringRightOfBrac=
ket)
+                        if match:
+                            indexOfNextSymbol =3D match.start()
+                            stringRepOfInternalNode =3D stringRightOfBrack=
et[:indexOfNextSymbol]
+                            internalNodes =3D self._makeNodesFromString( s=
tringRepOfInternalNode, depth)
+                            if len(internalNodes) > 0:
+                                InternalNode =3D internalNodes[0]
+                            lenOfPreceedingInternalNodeString =3D len(stri=
ngRepOfInternalNode)
+                        else:   # sometimes the node can be the last eleme=
nt of a string
+                            InternalNode =3D self._makeNodesFromString(str=
ing[j+1:], depth)[0]
+                            lenOfPreceedingInternalNodeString =3D len(stri=
ng) - j
+                    if InternalNode =3D=3D None:       #creating a generic=
 node if it is unnamed
+                        InternalNode =3D self.phyloTree.makeNode( "", dept=
h=3Ddepth, isInternal=3DTrue ) #"internal-" + str(depth)
+                        lenOfPreceedingInternalNodeString =3D 0
+
+                    # recussive call to make the internal claude
+                    childSubString =3D string[ i + 1 : j ]
+                    InternalNode.addChildNode(self.parseNode(childSubStrin=
g, depth + 1))
+
+                    nodes.append(InternalNode)  # we append the internal n=
ode later to preserve order
+
+                    start =3D j + 1
+                continue
+
+        if depth =3D=3D 0:    # if its the root node, we do nothing about =
it and return
+            return nodes[0]
+
+        # Adding last most set of children
+        endString =3D string[start:]
+        if string[start-1] =3D=3D ")":  # if the symbol belongs to an inte=
rnal node which is created previously, then we remove it from the string le=
ft to parse
+            match =3D re.search(r"[\)\,\(]", endString)
+            if match:
+                endOfNodeName =3D start + match.start() + 1
+                endString =3D string[endOfNodeName:]
+                nodes +=3D self._makeNodesFromString(endString, depth)
+
+        return nodes


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/visualization/phyloviz/nexusparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/nexusparser.py
@@ -0,0 +1,107 @@
+from newickparser import Newick_Parser
+import re
+
+MAX_READLINES =3D 200000
+
+
+class Nexus_Parser(Newick_Parser):
+
+    def __init__(self):
+        super(Nexus_Parser, self).__init__()
+
+    def parseFile(self, filePath):
+        """passes a file and extracts its Nexus content."""
+        return self.parseNexus(filePath)
+
+
+    def parseNexus(self, filename):
+        """ Nexus data is stored in blocks between a line starting with be=
gin and another line starting with end;
+        Commends inside square brackets are to be ignored,
+        For more information: http://wiki.christophchamp.com/index.php/NEX=
US_file_format
+        Nexus can store multiple trees
+        """
+
+        with open( filename, "rt") as nex_file:
+            nexlines =3D nex_file.readlines()
+
+        rowCount =3D 0
+        inTreeBlock =3D False         # sentinel to check if we are in a t=
ree block
+        intranslateBlock =3D False    # sentinel to check if we are in the=
 translate region of the tree. Stores synonyms of the labellings
+        self.inCommentBlock =3D False
+        self.nameMapping =3D None       # stores mapping representation us=
ed in nexus format
+        treeNames =3D []
+
+        for line in nexlines:
+            line =3D line.replace(";\n", "")
+            lline =3D line.lower()
+
+            if rowCount > MAX_READLINES or (not nex_file) :
+                break
+            rowCount +=3D1
+            # We are only interested in the tree block.
+            if "begin" in lline and "tree" in lline and not inTreeBlock:
+                inTreeBlock =3D True
+                continue
+            if inTreeBlock and "end" in lline[:3]:
+                inTreeBlock, currPhyloTree =3D False, None
+                continue
+
+            if inTreeBlock:
+
+                if "title" in lline:        # Adding title to the tree
+                    titleLoc =3D lline.find("title")
+                    title =3D line[titleLoc + 5:].replace(" ", "")
+
+                    continue
+
+                if "translate" in lline:
+                    intranslateBlock =3D True
+                    self.nameMapping =3D {}
+                    continue
+
+                if intranslateBlock:
+                    mappingLine =3D self.splitLinebyWhitespaces(line)
+                    key, value =3D mappingLine[1], mappingLine[2].replace(=
",", "").replace("'","")    #replacing illegal json characters
+                    self.nameMapping[key] =3D value
+
+                # Extracting newick Trees
+                if "tree" in lline:
+                    intranslateBlock =3D False
+
+                    treeLineCols =3D self.splitLinebyWhitespaces(line)
+                    treeName, newick =3D treeLineCols[2], treeLineCols[-1]
+
+                    if newick =3D=3D "":    # Empty lines can be found in =
tree blocks
+                        continue
+
+                    currPhyloTree =3D self._parseNewickToJson(newick, tree=
Name, nameMap=3Dself.nameMapping)
+
+                    self.phyloTrees.append(currPhyloTree)
+                    treeIndex =3D len(self.phyloTrees) - 1
+                    treeNames.append( (treeName, treeIndex) )    # appendi=
ng name of tree, and its index
+                    continue
+
+        return self.phyloTrees, treeNames
+
+
+    def splitLinebyWhitespaces(self, line):
+        """replace tabs and write spaces to a single write space, so we ca=
n properly split it."""
+        return re.split(r"\s+", line)
+
+
+    def checkComments(self, line):
+        """Check to see if the line/lines is a comment."""
+        if not self.inCommentBlock:
+            if "[" in line:
+                if "]" not in line:
+                    self.inCommentBlock =3D True
+                else:
+                    return "Nextline"   # need to move on to the nextline =
after getting out of comment
+        else :
+            if "]" in line:
+                if line.rfind("[") > line.rfind("]"):
+                    pass                # a comment block is closed but an=
other is open.
+                else:
+                    self.inCommentBlock =3D False
+                    return "Nextline"   # need to move on to the nextline =
after getting out of comment
+        return ""
\ No newline at end of file


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py
@@ -0,0 +1,35 @@
+from newickparser import Newick_Parser
+from nexusparser import Nexus_Parser
+from phyloxmlparser import Phyloxml_Parser
+
+class Phyloviz_DataProvider(object):
+
+    def __init__(self):
+        pass
+
+    def parseFile(self, filepath, fileExt):
+        """returns [trees], meta
+            Trees are actually an array of JsonDicts. It's usually one tre=
e, except in the case of Nexus
+        """
+        jsonDicts, meta =3D [], {}
+        try:
+            if fileExt =3D=3D "nhx": # parses newick files
+                newickParser =3D Newick_Parser()
+                jsonDicts, parseMsg =3D newickParser.parseFile(filepath)
+            elif fileExt =3D=3D "phyloxml": # parses phyloXML files
+                phyloxmlParser =3D Phyloxml_Parser()
+                jsonDicts, parseMsg =3D phyloxmlParser.parseFile(filepath)
+            elif fileExt =3D=3D "nex": # parses nexus files
+                nexusParser =3D Nexus_Parser()
+                jsonDicts, parseMsg =3D nexusParser.parseFile(filepath)
+                meta["trees"] =3D parseMsg
+            else:
+                raise Exception("File type is not supported")
+
+            meta["msg"] =3D parseMsg
+
+        except Exception:
+            jsonDicts, meta["msg"] =3D [], "Parse failed"
+
+        return jsonDicts, meta
+


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/visualization/phyloviz/phyloxmlparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py
@@ -0,0 +1,145 @@
+from baseparser import Base_Parser, PhyloTree, Node
+from lxml import etree
+
+class Phyloxml_Parser(Base_Parser):
+    """Parses a phyloxml file into a json file that will be passed to Phyl=
oViz for display"""
+
+    def __init__(self):
+        super(Phyloxml_Parser, self).__init__()
+        self.phyloTree =3D PhyloTree()
+        self.tagsOfInterest =3D {
+            "clade": "",
+            "name" : "name",
+            "branch_length" : "length",
+            "confidence"    : "bootstrap",
+            "events"        : "events"
+        }
+
+    def parseFile(self, filePath):
+        """passes a file and extracts its Phylogeny Tree content."""
+        phyloXmlFile =3D open(filePath, "r")
+
+        xmlTree =3D etree.parse(phyloXmlFile)
+        xmlRoot =3D xmlTree.getroot()[0]
+        self.nameSpaceIndex =3D xmlRoot.tag.rfind("}") + 1 # used later by=
 the clean tag method to remove the name space in every element.tag
+
+        phyloRoot =3D None
+        for child in xmlRoot:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "clade":
+                phyloRoot =3D child
+            elif childTag =3D=3D "name":
+                self.phyloTree.title =3D child.text
+
+        self.phyloTree.root =3D self.parseNode(phyloRoot, 0)
+        jsonDict =3D self.phyloTree.generateJsonableDict()
+        return [jsonDict], "Success"
+
+
+    def parseNode(self, node, depth):
+        """Parses any node within a phyloxml tree and looks out for claude=
, which signals the creation of
+        nodes - internal OR leaf"""
+        assert isinstance(node, etree._Element)
+
+        tag =3D self.cleanTag(node.tag)
+        if not tag =3D=3D "clade":
+            return None
+        hasInnerClade =3D False
+
+        # peeking once for parent and once for child to check if the node =
is internal
+        for child in node:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "clade":
+                hasInnerClade =3D True
+                break
+
+        if hasInnerClade:       # this node is an internal node
+            currentNode =3D self._makeInternalNode(node, depth=3D depth)
+            for child in node:
+                child =3D self.parseNode(child, depth + 1)
+                if isinstance(child, Node):
+                    currentNode.addChildNode(child)
+
+        else:                   # this node is a leaf node
+            currentNode =3D self._makeLeafNode(node, depth=3Ddepth+1)
+
+        return currentNode
+
+
+    def _makeLeafNode(self, leafNode, depth =3D 0 ):
+        """Makes leaf nodes by calling Phylotree methods"""
+        node =3D {}
+        for child in leafNode:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag in self.tagsOfInterest:
+                key =3D self.tagsOfInterest[childTag]    # need to map phy=
loxml terms to ours
+                node[key] =3D child.text
+
+        node["depth"] =3D depth
+        return self.phyloTree.makeNode(self._getNodeName(leafNode), **node)
+
+    def _getNodeName(self, node, depth=3D-1):
+        """Gets the name of a claude. It handles the case where a taxonomy=
 node is involved"""
+
+        def getTagFromTaxonomyNode(node):
+            """Returns the name of a taxonomy node. A taxonomy node have t=
o be treated differently as the name
+            is embedded one level deeper"""
+            phyloxmlTaxoNames =3D {
+                "common_name" : "",
+                "scientific_name" : "",
+                "code"  : ""
+            }
+            for child in node:
+                childTag =3D self.cleanTag(child.tag)
+                if childTag in phyloxmlTaxoNames:
+                    return child.text
+            return ""
+
+        nodeName =3D ""
+        for child in node:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "name" :
+                nodeName =3D child.text
+                break
+            elif childTag =3D=3D "taxonomy":
+                nodeName =3D getTagFromTaxonomyNode(child)
+                break
+
+        return nodeName
+
+
+    def _makeInternalNode(self, internalNode, depth=3D0):
+        """ Makes an internal node from an element object that is gurantee=
d to be a parent node.
+        Gets the value of interests like events and appends it to a custom=
 node object that will be passed to PhyloTree to make nodes
+        """
+        node =3D {}
+        for child in internalNode:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "clade":
+                continue
+            elif childTag in self.tagsOfInterest:
+                if childTag =3D=3D "events":    # events is nested 1 more =
level deeper than others
+                    key, text =3D "events", self.cleanTag(child[0].tag)
+                else:
+                    key =3D self.tagsOfInterest[childTag]
+                    text =3D child.text
+                node[key] =3D text
+
+
+        return self.phyloTree.makeNode(self._getNodeName(internalNode, dep=
th), **node)
+
+
+    def cleanTag(self, tagString):
+        return tagString[self.nameSpaceIndex:]
+
+
+if __name__=3D=3D"__main__":
+
+    # Files tested against
+    parser =3D Phyloxml_Parser()
+    filepath =3D "../data/" +"apaf.xml"
+    #    filepath =3D "../data/" +"12_multiple_supports.xml"
+
+    #    filepath =3D "../data/" +"bcl_2.xml"
+    #    filepath =3D "../data/" +"reducedXml.xml"
+    parser.parseFile(filepath)


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/web/controllers/phyloviz.py
--- /dev/null
+++ b/lib/galaxy/web/controllers/phyloviz.py
@@ -0,0 +1,97 @@
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+from galaxy.util.json import to_json_string, from_json_string
+from galaxy.web.base.controller import *
+from galaxy.visualization.phyloviz.phyloviz_dataprovider import Phyloviz_D=
ataProvider
+
+
+class PhyloVizController( BaseUIController, UsesVisualizationMixin, UsesHi=
storyDatasetAssociationMixin, SharableMixin ):
+    """
+    Controller for phyloViz browser interface.
+    """
+    def __init__(self, app ):
+        BaseUIController.__init__( self, app )
+
+    @web.expose
+    @web.require_login()
+    def index( self, trans, dataset_id =3D None, **kwargs ):
+        """
+        The index method is called using phyloviz/ with a dataset id passe=
d in.
+        The relevant data set is then retrieved via get_json_from_datasetI=
d which interfaces with the parser
+        The json representation of the phylogenetic tree along with the co=
nfig is then written in the .mako template and passed back to the user
+        """
+        json, config =3D self.get_json_from_datasetId(trans, dataset_id)
+        config["saved_visualization"] =3D False
+        return trans.fill_template( "visualization/phyloviz.mako", data =
=3D json, config=3Dconfig)
+
+
+    @web.expose
+    def visualization(self, trans, id):
+        """
+        Called using a viz_id (id) to retrieved stored visualization data =
(in json format) and all the viz_config
+        """
+        viz =3D self.get_visualization(trans, id)
+        config =3D self.get_visualization_config(trans, viz)
+        config["saved_visualization"] =3D True
+        data =3D config["root"]
+
+        return trans.fill_template( "visualization/phyloviz.mako", data =
=3D data, config=3Dconfig)
+
+
+    @web.expose
+    @web.json
+    def load_visualization_json(self, trans, viz_id):
+        """
+        Though not used in current implementation, this provides user with=
 a convenient method to retrieve the viz_data & viz_config via json.
+        """
+        viz =3D self.get_visualization(trans, viz_id)
+        viz_config =3D self.get_visualization_config(trans, viz)
+        viz_config["saved_visualization"] =3D True
+        return {
+            "data" : viz_config["root"],
+            "config" : viz_config
+        }
+
+
+    @web.expose
+    @web.json
+    def getJsonData(self, trans, dataset_id, treeIndex=3D0):
+        """
+        Method to retrieve data asynchronously via json format. Retriving =
from here rather than
+        making a direct datasets/ call allows for some processing and even=
t capturing
+        """
+        treeIndex =3D int(treeIndex)
+        json, config =3D self.get_json_from_datasetId(trans, dataset_id, t=
reeIndex)
+        packedJson =3D {
+            "data" : json,
+            "config" : config
+        }
+
+        return packedJson
+
+
+    def get_json_from_datasetId(self, trans, dataset_id, treeIndex=3D0):
+        """
+        For interfacing phyloviz controllers with phyloviz visualization d=
ata provider (parsers)
+        """
+        dataset =3D self.get_dataset(trans, dataset_id)
+        fileExt, filepath  =3D dataset.ext, dataset.file_name      # .name=
 stores the name of the dataset from the orginal upload
+        json, config =3D "", {}         #        config contains propertie=
s of the tree and file
+
+        if fileExt =3D=3D "json":
+            something, json =3D self.get_data(dataset)
+        else:
+            try:
+                pd =3D Phyloviz_DataProvider()
+                json, config =3D pd.parseFile(filepath, fileExt)
+                json =3D json[treeIndex]
+            except Exception:
+                pass
+
+        config["title"] =3D dataset.display_name()
+        config["ext"] =3D fileExt
+        config["dataset_id"] =3D dataset_id
+        config["treeIndex"] =3D treeIndex
+
+        return json, config


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -16,6 +16,10 @@
             action =3D "paramamonster"
         elif item.type =3D=3D "circster":
             action =3D "circster"
+        elif item.type =3D=3D "phyloviz":
+            # Support phyloviz
+            controller =3D "phyloviz"
+            action =3D "visualization"
         return dict( controller=3Dcontroller, action=3Daction, id=3Ditem.i=
d )
=20
     # Grid definition


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 static/scripts/viz/phyloviz.js
--- /dev/null
+++ b/static/scripts/viz/phyloviz.js
@@ -0,0 +1,955 @@
+var UserMenuBase =3D Backbone.View.extend({
+    /**
+     * Base class of any menus that takes in user interaction. Contains ch=
ecking methods.
+     */
+
+    className: 'UserMenuBase',
+
+    isAcceptableValue : function ($inputKey, min, max) {
+        /**
+         * Check if an input value is a number and falls within max min.
+         */
+        var self =3D this,
+            value =3D $inputKey.val(),
+            fieldName =3D $inputKey.attr("displayLabel") || $inputKey.attr=
("id").replace("phyloViz", "");
+
+        function isNumeric(n) {
+            return !isNaN(parseFloat(n)) && isFinite(n);
+        }
+
+        if (!isNumeric(value)){
+            alert(fieldName + " is not a number!");
+            return false;
+        }
+
+        if ( value > max){
+            alert(fieldName + " is too large.");
+            return false;
+        } else if ( value < min) {
+            alert(fieldName + " is too small.");
+            return false;
+        }
+        return true;
+    },
+
+    hasIllegalJsonCharacters : function($inputKey) {
+        /**
+         * Check if any user string inputs has illegal characters that jso=
n cannot accept
+         */
+        if ($inputKey.val().search(/"|'|\\/) !=3D=3D -1){
+            alert("Named fields cannot contain these illegal characters: d=
ouble quote(\"), single guote(\'), or back slash(\\). ");
+            return true;
+        }
+        return false;
+    }
+});
+
+
+function PhyloTreeLayout() {
+    /**
+     * -- Custom Layout call for phyloViz to suit the needs of a phylogene=
tic tree.
+     * -- Specifically: 1) Nodes have a display display of (=3D evo dist X=
 depth separation) from their parent
+     *                  2) Nodes must appear in other after they have expa=
nd and contracted
+     */
+
+    var self =3D this,
+        hierarchy =3D d3.layout.hierarchy().sort(null).value(null),
+        height =3D 360, // ! represents both the layout angle and the heig=
ht of the layout, in px
+        layoutMode =3D "Linear",
+        leafHeight =3D 18, // height of each individual leaf node
+        depthSeparation =3D 200, // separation between nodes of different =
depth, in px
+        leafIndex =3D 0, // change to recurssive call
+        defaultDist =3D 0.5, // tree defaults to 0.5 dist if no dist is sp=
ecified
+        maxTextWidth =3D 50; // maximum length of the text labels
+
+
+    self.leafHeight =3D function(inputLeafHeight){
+        if (typeof inputLeafHeight =3D=3D=3D "undefined"){ return leafHeig=
ht; }
+        else { leafHeight =3D inputLeafHeight; return self;}
+    };
+
+    self.layoutMode =3D function(mode){
+        if (typeof mode =3D=3D=3D "undefined"){ return layoutMode; }
+        else { layoutMode =3D mode; return self;}
+    };
+
+    self.layoutAngle =3D function(angle) {    // changes the layout angle =
of the display, which is really changing the height
+        if (typeof angle =3D=3D=3D "undefined"){ return height; }
+        if (isNaN(angle) || angle < 0 || angle > 360) { return self; } // =
to use default if the user puts in strange values
+        else { height =3D angle; return self;}
+    };
+
+    self.separation =3D function(dist){   // changes the dist between the =
nodes of different depth
+        if (typeof dist =3D=3D=3D "undefined"){ return depthSeparation; }
+        else { depthSeparation =3D dist; return self;}
+    };
+
+    self.links =3D function (nodes) {     // uses d3 native method to gene=
rate links. Done.
+        return d3.layout.tree().links(nodes);
+    };
+
+    // -- Custom method for laying out phylogeny tree in a linear fashion
+    self.nodes =3D function (d, i) {
+        var _nodes =3D hierarchy.call(self, d, i),         // self is to f=
ind the depth of all the nodes, assumes root is passed in
+            nodes =3D [],
+            maxDepth =3D 0,
+            numLeaves =3D 0;
+
+        // changing from hierarchy's custom format for data to usable form=
at
+        _nodes.forEach(function (_node){
+            var node =3D _node.data;
+            node.depth =3D _node.depth;
+            maxDepth =3D node.depth > maxDepth ? node.depth : maxDepth;  /=
/finding max depth of tree
+            nodes.push(node);
+        });
+        // counting the number of leaf nodes and assigning max depth to no=
des that do not have children to flush all the leave nodes
+        nodes.forEach(function(node){
+            if ( !node.children )  { //&& !node._children
+                numLeaves +=3D 1;
+                node.depth =3D maxDepth; // if a leaf has no child it woul=
d be assigned max depth
+            }
+        });
+
+        leafHeight =3D layoutMode =3D=3D=3D "Circular" ? height / numLeave=
s : leafHeight;
+        leafIndex =3D 0;
+        layout(nodes[0], maxDepth, leafHeight, null);
+
+        return nodes;
+    };
+
+
+    function layout (node, maxDepth, vertSeparation, parent) {
+        /**
+         * -- Function with side effect of adding x0, y0 to all child; tak=
e in the root as starting point
+         *  assuming that the leave nodes would be sorted in presented ord=
er
+         *          horizontal(y0) is calculated according to (=3D evo dis=
t X depth separation) from their parent
+         *          vertical (x0) - if leave node: find its order in all o=
f the  leave node =3D=3D=3D node.id, then multiply by verticalSeparation
+         *                  - if parent node: is place in the mid point al=
l of its children nodes
+         * -- The layout will first calculate the y0 field going towards t=
he leaves, and x0 when returning
+         */
+        var children =3D node.children,
+            sumChildVertSeparation =3D 0;
+
+        // calculation of node's dist from parents, going down.
+        var dist =3D node.dist || defaultDist;
+        dist =3D dist > 1 ? 1 : dist;     // We constrain all dist to be l=
ess than one
+        node.dist =3D dist;
+        if (parent !=3D=3D null){
+            node.y0 =3D parent.y0 + dist * depthSeparation;
+        } else {    //root node
+            node.y0 =3D maxTextWidth;
+        }
+
+
+        // if a node have no children, we will treat it as a leaf and star=
t laying it out first
+        if (!children) {
+            node.x0 =3D leafIndex++ * vertSeparation;
+        } else {
+            // if it has children, we will visit all its children and calc=
ulate its position from its children
+            children.forEach( function (child) {
+                child.parent =3D node;
+                sumChildVertSeparation +=3D layout(child, maxDepth, vertSe=
paration, node);
+            });
+            node.x0 =3D sumChildVertSeparation / children.length;
+        }
+
+        // adding properties to the newly created node
+        node.x =3D node.x0;
+        node.y =3D node.y0;
+        return node.x0;
+    }
+    return self;
+}
+
+
+/**
+ * -- PhyloTree Model --
+ */
+var PhyloTree =3D Visualization.extend({
+    defaults : {
+        layout: "Linear",
+        separation : 250,    // px dist between nodes of different depth t=
o represent 1 evolutionary until
+        leafHeight: 18,
+        type : "phyloviz",   // visualization type
+        title : "Title",
+        scaleFactor: 1,
+        translate: [0,0],
+        fontSize: 12,        //fontSize of node label
+        selectedNode : null,
+        nodeAttrChangedTime : 0
+    },
+
+    root : {}, // Root has to be its own independent object because it is =
not part of the viz_config
+
+    toggle : function (d) {
+        /**
+         * Mechanism to expand or contract a single node. Expanded nodes h=
ave a children list, while for
+         * contracted nodes the list is stored in _children. Nodes with th=
eir children data stored in _children will not have their
+         * children rendered.
+         */
+        if(typeof d =3D=3D=3D "undefined") {return ;}
+        if (d.children ) {
+            d._children =3D d.children;
+            d.children =3D null;
+        } else {
+            d.children =3D d._children;
+            d._children =3D null;
+        }
+    },
+
+    toggleAll : function(d) {
+        /**
+         *  Contracts the phylotree to a single node by repeatedly calling=
 itself to place all the list
+         *  of children under _children.
+         */
+        if (d.children && d.children.length !=3D=3D 0) {
+            d.children.forEach(this.toggleAll);
+            toggle(d);
+        }
+    },
+
+    getData : function (){
+        /**
+         *  Return the data of the tree. Used for preserving state.
+         */
+        return this.root;
+    },
+
+    save: function() {
+        /**
+         * Overriding the default save mechanism to do some clean of circu=
lar reference of the
+         * phyloTree and to include phyloTree in the saved json
+         */
+        var root =3D this.root;
+        cleanTree(root);
+        this.set("root", root);
+
+        function cleanTree(node){
+            // we need to remove parent to delete circular reference
+            delete node.parent;
+
+            // removing unnecessary attributes
+            if (node._selected){ delete node._selected;}
+
+            node.children ? node.children.forEach(cleanTree) : 0;
+            node._children ? node._children.forEach(cleanTree) : 0;
+        }
+
+        var config  =3D jQuery.extend(true, {}, this.attributes);
+        config["selectedNode"] =3D null;
+
+        show_message("Saving to Galaxy", "progress");
+
+        return $.ajax({
+            url: this.url(),
+            type: "POST",
+            dataType: "json",
+            data: {
+                vis_json: JSON.stringify(config)
+            },
+            success: function(res){
+                var viz_id =3D res.url.split("id=3D")[1].split("&")[0],
+                    viz_url =3D "/phyloviz/visualization?id=3D" + viz_id;
+                window.history.pushState({}, "", viz_url + window.location=
.hash);
+                hide_modal();
+            }
+        });
+    }
+});
+
+
+
+/**
+ * -- Views --
+ */
+var PhylovizLayoutBase =3D  Backbone.View.extend({
+    /**
+     *  Stores the default variable for setting up the visualization
+     */
+    defaults : {
+        nodeRadius : 4.5 // radius of each node in the diagram
+    },
+
+
+    stdInit : function (options) {
+        /**
+         *  Common initialization in layouts
+         */
+
+        var self =3D this;
+        self.model.on("change:separation change:leafHeight change:fontSize=
 change:nodeAttrChangedTime", self.updateAndRender, self);
+
+        self.vis =3D options.vis;
+        self.i =3D 0;
+        self.maxDepth =3D -1; // stores the max depth of the tree
+
+        self.width =3D options.width;
+        self.height =3D options.height;
+    },
+
+
+    updateAndRender : function(source) {
+        /**
+         *  Updates the visualization whenever there are changes in the ex=
pansion and contraction of nodes
+         *  AND possibly when the tree is edited.
+         */
+        var vis =3D d3.select(".vis"),
+            self =3D this;
+        source =3D source || self.model.root;
+
+        self.renderNodes(source);
+        self.renderLinks(source);
+        self.addTooltips();
+    },
+
+
+    renderLinks : function(source) {
+        /**
+         * Renders the links for the visualization.
+         */
+        var self =3D this;
+        var diagonal =3D self.diagonal;
+        var duration =3D self.duration;
+        var layoutMode =3D self.layoutMode;
+        var link =3D self.vis.selectAll("g.completeLink")
+            .data(self.tree.links(self.nodes), function(d) { return d.targ=
et.id; });
+
+        var calcalateLinePos =3D function(d) {
+            d.pos0 =3D d.source.y0 + " " + d.source.x0;   // position of t=
he source node <=3D> starting location of the line drawn
+            d.pos1 =3D d.source.y0 + " " + d.target.x0;  // position where=
 the line makes a right angle bend
+            d.pos2 =3D d.target.y0 + " " + d.target.x0;     // point where=
 the horizontal line becomes a dotted line
+        };
+
+        var linkEnter =3D link.enter().insert("svg:g","g.node")
+            .attr("class", "completeLink");
+
+
+        linkEnter.append("svg:path")
+            .attr("class", "link")
+            .attr("d", function(d) {
+                calcalateLinePos(d);
+                return "M " + d.pos0  + " L " + d.pos1;
+            });
+
+        var linkUpdate =3D link.transition().duration(500);
+
+        linkUpdate.select("path.link")
+            .attr("d", function(d) {
+                calcalateLinePos(d);
+                return "M " + d.pos0 + " L " + d.pos1 + " L " + d.pos2;
+            });
+
+        var linkExit =3D link.exit().remove();
+
+    },
+
+    // User Interaction methods below
+
+    selectNode : function(node){
+        /**
+         *  Displays the information for editting
+         */
+        var self =3D this;
+        d3.selectAll("g.node")
+            .classed("selectedHighlight", function(d){
+                if (node.id =3D=3D=3D d.id){
+                    if(node._selected) { // for de=3Dselecting node.
+                        delete node._selected;
+                        return false;
+                    } else {
+                        node._selected =3D true;
+                        return true;
+                    }
+                }
+                return false;
+            });
+
+        self.model.set("selectedNode", node);
+        $("#phyloVizSelectedNodeName").val(node.name);
+        $("#phyloVizSelectedNodeDist").val(node.dist);
+        $("#phyloVizSelectedNodeAnnotation").val(node.annotation || "");
+    },
+
+    addTooltips : function (){
+        /**
+         *  Creates bootstrap tooltip for the visualization. Has to be cal=
led repeatedly due to newly generated
+         *  enterNodes
+         */
+        $(".bs-tooltip").remove();      //clean up tooltip, just in case i=
ts listeners are removed by d3
+        $(".node")
+            .attr("data-original-title", function(){
+                var d =3D this.__data__,
+                    annotation =3D d.annotation || "None" ;
+                return d ? (d.name ? d.name + "<br/>" : "") + "Dist: " + d=
.dist + " <br/>Annotation: " + annotation: "";
+            })
+            .tooltip({'placement':'top', 'trigger' : 'hover'});
+
+    }
+});
+
+
+
+
+var PhylovizLinearView =3D  PhylovizLayoutBase.extend({
+    /**
+     * Linea layout class of Phyloviz, is responsible for rendering the no=
des
+     * calls PhyloTreeLayout to determine the positions of the nodes
+     */
+    initialize : function(options){
+        // Default values of linear layout
+        var self =3D this;
+        self.margins =3D options.margins;
+        self.layoutMode =3D "Linear";
+
+        self.stdInit(options);
+
+        self.layout();
+        self.updateAndRender(self.model.root);
+    },
+
+    layout : function() {
+        /**
+         * Creates the basic layout of a linear tree by precalculating fix=
ed values.
+         * One of calculations are also made here
+         */
+
+        var self =3D this;
+
+        self.tree =3D new PhyloTreeLayout().layoutMode("Linear");
+        self.diagonal =3D d3.svg.diagonal()
+            .projection(function(d) { return [d.y, d.x ]; });
+    },
+
+    renderNodes : function (source) {
+        /**
+         * Renders the nodes base on Linear layout.
+         */
+        var self =3D this,
+            fontSize =3D self.model.get("fontSize") + "px";
+
+        // assigning properties from models
+        self.tree.separation(self.model.get("separation")).leafHeight(self=
.model.get("leafHeight"));
+
+        var duration =3D 500,
+            nodes =3D self.tree.separation(self.model.get("separation")).n=
odes(self.model.root);
+
+        var node =3D self.vis.selectAll("g.node")
+            .data(nodes, function(d) { return d.name + d.id || (d.id =3D +=
+self.i); });
+
+        // These variables has to be passed into update links which are in=
 the base methods
+        self.nodes =3D nodes;
+        self.duration =3D duration;
+
+        // ------- D3 ENTRY --------
+        // Enter any new nodes at the parent's previous position.
+        var nodeEnter =3D node.enter().append("svg:g")
+            .attr("class", "node")
+            .on("dblclick", function(){ d3.event.stopPropagation();    })
+            .on("click", function(d) {
+                if (d3.event.altKey) {
+                    self.selectNode(d);        // display info if alt is p=
ressed
+                } else {
+                    if(d.children && d.children.length =3D=3D=3D 0){ retur=
n;}  // there is no need to toggle leaves
+                    self.model.toggle(d);   // contract/expand nodes at da=
ta level
+                    self.updateAndRender(d);   // re-render the tree
+                }
+            });
+
+        nodeEnter.attr("transform", function(d) { return "translate(" + so=
urce.y0 + "," + source.x0 + ")"; });
+
+        nodeEnter.append("svg:circle")
+            .attr("r", 1e-6)
+            .style("fill", function(d) { return d._children ? "lightsteelb=
lue" : "#fff"; });
+
+        nodeEnter.append("svg:text")
+            .attr("class", "nodeLabel")
+            .attr("x", function(d) { return d.children || d._children ? -1=
0 : 10; })
+            .attr("dy", ".35em")
+            .attr("text-anchor", function(d) { return d.children || d._chi=
ldren ? "end" : "start"; })
+            .style("fill-opacity", 1e-6);
+
+        // ------- D3 TRANSITION --------
+        // Transition nodes to their new position.
+        var nodeUpdate =3D node.transition()
+            .duration(duration);
+
+        nodeUpdate.attr("transform", function(d) {
+            return "translate(" + d.y + "," + d.x + ")"; });
+
+        nodeUpdate.select("circle")
+            .attr("r", self.defaults.nodeRadius)
+            .style("fill", function(d) { return d._children ? "lightsteelb=
lue" : "#fff"; });
+
+        nodeUpdate.select("text")
+            .style("fill-opacity", 1)
+            .style("font-size", fontSize)
+            .text(function(d) { return d.name; });
+
+        // ------- D3 EXIT --------
+        // Transition exiting nodes to the parent's new position.
+        var nodeExit =3Dnode.exit().transition()
+            .duration(duration)
+            .remove();
+
+        nodeExit.select("circle")
+            .attr("r", 1e-6);
+
+        nodeExit.select("text")
+            .style("fill-opacity", 1e-6);
+
+        // Stash the old positions for transition.
+        nodes.forEach(function(d) {
+            d.x0 =3D d.x; // we need the x0, y0 for parents with children
+            d.y0 =3D d.y;
+        });
+    }
+
+});
+
+var PhylovizView =3D Backbone.View.extend({
+
+    className: 'phyloviz',
+
+    initialize: function(options) {
+        var self =3D this;
+        // -- Default values of the vis
+        self.MIN_SCALE =3D 0.05; //for zooming
+        self.MAX_SCALE =3D 5;
+        self.MAX_DISPLACEMENT =3D 500;
+        self.margins =3D [10, 60, 10, 80];
+
+        self.width =3D $("#PhyloViz").width();
+        self.height =3D $("#PhyloViz").height();
+        self.radius =3D self.width;
+        self.data =3D options.data;
+
+        // -- Events Phyloviz view responses to
+        $(window).resize(function(){
+            self.width =3D $("#PhyloViz").width();
+            self.height =3D $("#PhyloViz").height();
+            self.render();
+        });
+
+        // -- Create phyloTree model
+        self.phyloTree =3D new PhyloTree(options.config);
+        self.phyloTree.root =3D self.data;
+
+        // -- Set up UI functions of main view
+        self.zoomFunc =3D d3.behavior.zoom().scaleExtent([self.MIN_SCALE, =
self.MAX_SCALE]);
+        self.zoomFunc.translate(self.phyloTree.get("translate"));
+        self.zoomFunc.scale(self.phyloTree.get("scaleFactor"));
+
+        // -- set up header buttons, search and settings menu
+        self.navMenu =3D new HeaderButtons(self);
+        self.settingsMenu =3D new SettingsMenu({phyloTree : self.phyloTree=
});
+        self.nodeSelectionView =3D new NodeSelectionView({phyloTree : self=
.phyloTree});
+        self.search =3D new PhyloVizSearch();
+
+
+        setTimeout(function(){      // using settimeout to call the zoomAn=
dPan function according to the stored attributes in viz_config
+            self.zoomAndPan();
+        }, 1000);
+    },
+
+    render: function(){
+        // -- Creating helper function for vis. --
+        var self =3D this;
+        $("#PhyloViz").empty();
+
+        // -- Layout viz. --
+        self.mainSVG =3D d3.select("#PhyloViz").append("svg:svg")
+            .attr("width", self.width)
+            .attr("height", self.height)
+            .attr("pointer-events", "all")
+            .call(self.zoomFunc.on("zoom", function(){
+            self.zoomAndPan();
+        }));
+
+        self.boundingRect =3D self.mainSVG.append("svg:rect")
+            .attr("class", "boundingRect")
+            .attr("width", self.width)
+            .attr("height", self.height)
+            .attr("stroke", "black")
+            .attr("fill", "white");
+
+        self.vis =3D self.mainSVG
+            .append("svg:g")
+            .attr("class", "vis");
+
+        self.layoutOptions =3D {
+            model : self.phyloTree,
+            width : self.width,
+            height : self.height,
+            vis: self.vis,
+            margins: self.margins
+        };
+
+        // -- Creating Title
+        $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("t=
itle") + ":");
+
+        // -- Create Linear view instance --
+        var linearView =3D new PhylovizLinearView(self.layoutOptions)
+    },
+
+    zoomAndPan : function(event){
+        /**
+         * Function to zoom and pan the svg element which the entire tree =
is contained within
+         * Uses d3.zoom events, and extend them to allow manual updates an=
d keeping states in model
+         */
+        if (typeof event !=3D=3D "undefined") {
+            var zoomParams =3D event.zoom,
+                translateParams =3D event.translate;
+        }
+
+        var self =3D this,
+            scaleFactor =3D self.zoomFunc.scale(),
+            translationCoor =3D self.zoomFunc.translate(),
+            zoomStatement =3D "",
+            translateStatement =3D "";
+
+        // Do manual scaling.
+        switch (zoomParams) {
+            case "reset":
+                scaleFactor =3D 1.0;
+                translationCoor =3D [0,0]; break;
+            case "+":
+                scaleFactor *=3D 1.1; break;
+            case "-":
+                scaleFactor *=3D 0.9; break;
+            default:
+                if (typeof zoomParams =3D=3D=3D "number") {
+                    scaleFactor =3D zoomParams;
+                } else if (d3.event !=3D=3D null) {
+                    scaleFactor =3D d3.event.scale;
+                }
+        }
+        if (scaleFactor < self.MIN_SCALE || scaleFactor > self.MAX_SCALE) =
{ return;}
+        self.zoomFunc.scale(scaleFactor); //update scale Factor
+        zoomStatement =3D "translate(" +  self.margins[3] + "," + self.mar=
gins[0] + ")" +
+            " scale(" + scaleFactor + ")";
+
+        // Do manual translation.
+        if( d3.event !=3D=3D null) {
+            translateStatement =3D "translate(" + d3.event.translate + ")";
+        } else {
+            if(typeof translateParams !=3D=3D "undefined") {
+                var x =3D translateParams.split(",")[0];
+                var y =3D translateParams.split(",")[1];
+                if (!isNaN(x) && !isNaN(y)){
+                    translationCoor =3D [translationCoor[0] + parseFloat(x=
), translationCoor[1] + parseFloat(y)];
+                }
+            }
+            self.zoomFunc.translate(translationCoor);   // update zoomFunc
+            translateStatement =3D "translate(" + translationCoor + ")";
+        }
+
+        self.phyloTree.set("scaleFactor", scaleFactor);
+        self.phyloTree.set("translate", translationCoor);
+        self.vis.attr("transform", translateStatement + zoomStatement); //=
refers to the view that we are actually zooming
+    },
+
+
+    reloadViz : function() {
+        /**
+         * Primes the Ajax URL to load another Nexus tree
+         */
+        var self =3D this,
+            treeIndex =3D $("#phylovizNexSelector :selected").val(),
+            dataset_id =3D self.phyloTree.get("dataset_id"),
+            url =3D "phyloviz/getJsonData?dataset_id=3D" + dataset_id + "&=
treeIndex=3D" + String(treeIndex);
+        $.getJSON(url, function(packedJson){
+            window.initPhyloViz(packedJson.data, packedJson.config);
+        });
+    }
+});
+
+
+var HeaderButtons =3D Backbone.View.extend({
+
+    initialize : function(phylovizView){
+        var self =3D this;
+        self.phylovizView =3D phylovizView;
+
+        // Clean up code - if the class initialized more than once
+        $("#panelHeaderRightBtns").empty();
+        $("#phyloVizNavBtns").empty();
+        $("#phylovizNexSelector").off();
+
+        self.initNavBtns();
+        self.initRightHeaderBtns();
+
+        // Initial a tree selector in the case of nexus
+        $("#phylovizNexSelector").off().on("change",  function() {self.phy=
lovizView.reloadViz();}  );
+
+    },
+
+    initRightHeaderBtns : function(){
+        var self =3D this;
+
+        rightMenu =3D create_icon_buttons_menu([
+            { icon_class: 'gear', title: 'PhyloViz Settings', on_click: fu=
nction(){
+                $("#SettingsMenu").show();
+                self.settingsMenu.updateUI();
+            } },
+            { icon_class: 'disk', title: 'Save visualization', on_click: f=
unction() {
+                var nexSelected =3D $("#phylovizNexSelector option:selecte=
d").text();
+                if(nexSelected) {
+                    self.phylovizView.phyloTree.set("title", nexSelected);
+                }
+                self.phylovizView.phyloTree.save();
+            } },
+            { icon_class: 'chevron-expand', title: 'Search / Edit Nodes', =
on_click: function() {
+                $("#nodeSelectionView").show();
+            } },
+            { icon_class: 'information', title: 'Phyloviz Help', on_click:=
 function() {
+                window.open('http://wiki.g2.bx.psu.edu/Learn/Visualization=
/PhylogeneticTree');
+                // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs=
3EyMe1B1X_KFPouzIgrCz3zk/edit
+            } }
+        ],
+            {
+                tooltip_config: { placement: 'bottom' }
+            });
+        $("#panelHeaderRightBtns").append(rightMenu.$el);
+    },
+
+    initNavBtns: function() {
+        var self =3D this,
+            navMenu =3D create_icon_buttons_menu([
+                { icon_class: 'zoom-in', title: 'Zoom in', on_click: funct=
ion() {
+                    self.phylovizView.zoomAndPan({ zoom : "+"});
+                } },
+                { icon_class: 'zoom-out', title: 'Zoom out', on_click: fun=
ction() {
+                    self.phylovizView.zoomAndPan({ zoom : "-"});
+                } },
+                { icon_class: 'arrow-circle', title: 'Reset Zoom/Pan', on_=
click: function() {
+                    self.phylovizView.zoomAndPan({ zoom : "reset"});
+                } }
+            ],
+                {
+                    tooltip_config: { placement: 'bottom' }
+                });
+        $("#phyloVizNavBtns").append(navMenu.$el);
+    }
+});
+
+
+var SettingsMenu =3D UserMenuBase.extend({
+
+    className: 'Settings',
+
+    initialize: function(options){
+        // settings needs to directly interact with the phyloviz model so =
it will get access to it.
+        var self =3D this;
+        self.phyloTree =3D options.phyloTree;
+        self.el =3D $("#SettingsMenu");
+        self.inputs =3D {
+            separation : $("#phyloVizTreeSeparation"),
+            leafHeight : $("#phyloVizTreeLeafHeight"),
+            fontSize   : $("#phyloVizTreeFontSize")
+        };
+
+        //init all buttons of settings
+        $("#settingsCloseBtn").off().on("click", function() { self.el.hide=
(); });
+        $("#phylovizResetSettingsBtn").off().on("click", function() { self=
.resetToDefaults(); });
+        $("#phylovizApplySettingsBtn").off().on("click", function() { self=
.apply(); });
+    },
+
+    apply : function(){
+        /**
+         * Applying user values to phylotree model.
+         */
+        var self =3D this;
+        if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) ||
+            !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) ||
+            !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){
+            return;
+        }
+        $.each(self.inputs, function(key, $input){
+            self.phyloTree.set(key, $input.val());
+        });
+    },
+    updateUI : function(){
+        /**
+         * Called to update the values input to that stored in the model
+         */
+        var self =3D this;
+        $.each(self.inputs, function(key, $input){
+            $input.val(self.phyloTree.get(key));
+        });
+    },
+    resetToDefaults : function(){
+        /**
+         * Resets the value of the phyloTree model to its default
+         */
+        $(".bs-tooltip").remove();      // just in case the tool tip was n=
ot removed
+        var self =3D this;
+        $.each(self.phyloTree.defaults, function(key, value) {
+            self.phyloTree.set(key, value);
+        });
+        self.updateUI();
+    },
+
+    render: function(){
+
+    }
+
+});
+
+
+var NodeSelectionView =3D UserMenuBase.extend({
+    /**
+     * View for inspecting node properties and editing them
+     */
+    className: 'Settings',
+
+    initialize : function (options){
+        var self =3D this;
+        self.el =3D $("#nodeSelectionView");
+        self.phyloTree =3D options.phyloTree;
+
+        self.UI =3D {
+            enableEdit      : $('#phylovizEditNodesCheck'),
+            saveChanges     : $('#phylovizNodeSaveChanges'),
+            cancelChanges   : $("#phylovizNodeCancelChanges"),
+            name            : $("#phyloVizSelectedNodeName"),
+            dist            : $("#phyloVizSelectedNodeDist"),
+            annotation      : $("#phyloVizSelectedNodeAnnotation")
+        };
+
+        self.valuesOfConcern =3D {
+            name : null,
+            dist : null,
+            annotation : null
+        }; // temporarily stores the values in case user change their mind
+
+        //init UI buttons
+        $("#nodeSelCloseBtn").off().on("click", function() { self.el.hide(=
); });
+        self.UI.saveChanges.off().on("click", function(){ self.updateNodes=
(); });
+        self.UI.cancelChanges.off().on("click", function(){ self.cancelCha=
nges(); });
+
+        (function ($) {
+            // extending jquery fxn for enabling and disabling nodes.
+            $.fn.enable =3D function (isEnabled) {
+                return $(this).each(function () {
+                    if(isEnabled){
+                        $(this).removeAttr('disabled');
+                    } else {
+                        $(this).attr('disabled', 'disabled');
+                    }
+                });
+            };
+        })(jQuery);
+
+        self.UI.enableEdit.off().on("click", function () {
+            self.toggleUI();
+        });
+    },
+
+    toggleUI : function(){
+        /**
+         * For turning on and off the child elements
+         */
+        var self =3D this,
+            checked =3D self.UI.enableEdit.is(':checked');
+
+        !checked ? self.cancelChanges() : "";
+
+        $.each(self.valuesOfConcern, function(key, value) {
+            self.UI[key].enable(checked);
+        });
+        if(checked){
+            self.UI.saveChanges.show();
+            self.UI.cancelChanges.show();
+        } else {
+            self.UI.saveChanges.hide();
+            self.UI.cancelChanges.hide();
+        }
+
+    },
+
+    cancelChanges : function() {
+        /**
+         * Reverting to previous values in case user change their minds
+         */
+        var self =3D this,
+            node =3D self.phyloTree.get("selectedNode");
+        if (node){
+            $.each(self.valuesOfConcern, function(key, value) {
+                self.UI[key].val(node[key]);
+            });
+        }
+    },
+
+    updateNodes : function (){
+        /**
+         * Changing the data in the underlying tree with user-specified va=
lues
+         */
+        var self =3D this,
+            node =3D self.phyloTree.get("selectedNode");
+        if (node){
+            if (!self.isAcceptableValue(self.UI.dist, 0, 1) ||
+                self.hasIllegalJsonCharacters(self.UI.name) ||
+                self.hasIllegalJsonCharacters(self.UI.annotation) ) {
+                return;
+            }
+            $.each(self.valuesOfConcern, function(key, value) {
+                (node[key]) =3D self.UI[key].val();
+            });
+            self.phyloTree.set("nodeAttrChangedTime", new Date());
+        } else {
+            alert("No node selected");
+        }
+    }
+
+
+});
+
+
+
+var PhyloVizSearch =3D UserMenuBase.extend({
+    /**
+     * Initializes the search panel on phyloviz and handles its user inter=
action
+     * It allows user to search the entire free based on some qualifer, li=
ke dist <=3D val.
+     */
+    initialize : function () {
+        var self =3D this;
+
+        $("#phyloVizSearchBtn").on("click", function(){
+            var searchTerm =3D $("#phyloVizSearchTerm"),
+                searchConditionVal =3D $("#phyloVizSearchCondition").val()=
.split("-"),
+                attr =3D searchConditionVal[0],
+                condition =3D searchConditionVal[1];
+            self.hasIllegalJsonCharacters(searchTerm);
+
+            if (attr =3D=3D=3D "dist"){
+                self.isAcceptableValue(searchTerm, 0, 1);
+            }
+            self.searchTree(attr, condition, searchTerm.val());
+        });
+    },
+
+    searchTree : function (attr, condition, val){
+        /**
+         * Searches the entire tree and will highlight the nodes that matc=
h the condition in green
+         */
+        d3.selectAll("g.node")
+            .classed("searchHighlight", function(d){
+                var attrVal =3D  d[attr];
+                if (typeof attrVal !=3D=3D "undefined" && attrVal !=3D=3D =
null){
+                    if (attr =3D=3D=3D "dist"){
+                        switch (condition) {
+                            case "greaterEqual":
+                                return attrVal >=3D +val;
+                            case "lesserEqual":
+                                return attrVal <=3D +val;
+                            default:
+                                return;
+                        }
+
+                    } else if (attr =3D=3D=3D "name" || attr =3D=3D=3D "an=
notation") {
+                        return attrVal.toLowerCase().indexOf(val.toLowerCa=
se()) !=3D=3D -1;
+                    }
+                }
+            });
+    }
+});
\ No newline at end of file


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 templates/root/history.mako
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -272,6 +272,17 @@
     }
    =20
     init_trackster_links();
+
+    function init_phyloviz_links() {
+        // PhyloViz links
+        // Add to trackster browser functionality
+        $(".phyloviz-add").live("click", function() {
+            var dataset =3D this,
+                    dataset_jquery =3D $(this);
+            window.parent.location =3D dataset_jquery.attr("new-url");
+        });
+    }
+    init_phyloviz_links();
    =20
     // History rename functionality.
     async_save_text("history-name-container", "history-name", "${h.url_for=
( controller=3D"/history", action=3D"rename_async", id=3Dtrans.security.enc=
ode_id(history.id) )}", "new_name", 18);


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 templates/root/history_common.mako
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -29,6 +29,9 @@
 ## Render the dataset `data` as history item, using `hid` as the displayed=
 id
 <%def name=3D"render_dataset( data, hid, show_deleted_on_refresh =3D False=
, for_editing =3D True, display_structured =3D False )"><%
+
+        from galaxy.datatypes.xml import Phyloxml
+        from galaxy.datatypes.data import Newick, Nexus
         dataset_id =3D trans.security.encode_id( data.id )
=20
         if data.state in ['no state','',None]:
@@ -230,6 +233,14 @@
                                 action-url=3D"${h.url_for( controller=3D't=
racks', action=3D'browser', dataset_id=3Ddataset_id)}"
                                 new-url=3D"${h.url_for( controller=3D'trac=
ks', action=3D'index', dataset_id=3Ddataset_id, default_dbkey=3Ddata.dbkey)=
}" title=3D"View in Trackster"></a>
                         %endif
+                        <%
+                            isPhylogenyData =3D isinstance(data.datatype, =
 (Phyloxml, Nexus, Newick))
+                        %>
+                        %if isPhylogenyData:
+                                <a href=3D"javascript:void(0)"  class=3D"i=
con-button chart_curve phyloviz-add"
+                                   action-url=3D"${h.url_for( controller=
=3D'phyloviz', action=3D'-', dataset_id=3Ddataset_id)}"
+                                   new-url=3D"${h.url_for( controller=3D'p=
hyloviz', action=3D'index', dataset_id=3Ddataset_id)}" title=3D"View in Phy=
loviz"></a>
+                        %endif
                         %if trans.user:
                             %if not display_structured:
                                 <div style=3D"float: right">


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 templates/visualization/phyloviz.mako
--- /dev/null
+++ b/templates/visualization/phyloviz.mako
@@ -0,0 +1,320 @@
+<%inherit file=3D"/webapps/galaxy/base_panels.mako"/>
+##
+<%def name=3D"init()">
+    <%
+        self.has_left_panel=3DFalse
+        self.has_right_panel=3DFalse
+        self.active_view=3D"visualization"
+        self.message_box_visible=3DFalse
+    %>
+</%def>
+
+<%def name=3D"stylesheets()">
+    ${parent.stylesheets()}
+    <style>
+
+        .node circle {
+            cursor: pointer;
+            fill: #fff;
+            stroke: steelblue;
+            stroke-width: 1.5px;
+        }
+
+        .node.searchHighlight circle {
+            stroke-width: 3px;
+            stroke: #7adc26;
+        }
+
+        .node.selectedHighlight circle {
+            stroke-width: 3px;
+            stroke: #dc143c;
+        }
+
+        path.link {
+            fill: none;
+            stroke: #B5BBFF;
+            stroke-width: 4.0px;
+        }
+
+
+        div #phyloVizNavContainer{
+            text-align: center;
+            width: 100%;
+            height: 0px;
+        }
+
+        div #phyloVizNav{
+            font-weight: bold;
+            display: inline-block;
+            background: transparent;
+            top: -2em;
+            position: relative;
+        }
+
+        div .navControl{
+            float: left;
+        }
+
+        div#FloatingMenu {
+            left: 0;
+            top: 15%;
+            width:20%;
+            z-index:100;
+            padding: 5px;
+
+        }
+
+        div#SettingsMenu {
+            width: 25%;
+            top: 350px;
+
+        }
+
+        div#nodeSelectionView {
+            width: 25%;
+            top:70px;
+        }
+
+        .Panel {
+            right: 0%;
+            z-index: 101;
+            position: fixed;
+
+        ##          Borrowed from galaxy modal_dialogues
+                    background-color: white;
+            border: 1px solid #999;
+            border: 1px solid rgba(0, 0, 0, 0.3);
+            -webkit-border-radius: 6px;
+            -moz-border-radius: 6px;
+            border-radius: 6px;
+            -webkit-border-radius: 6px;
+            -moz-border-radius: 6px;
+            border-radius: 6px;
+            -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -webkit-background-clip: padding-box;
+            -moz-background-clip: padding-box;
+            background-clip: padding-box;
+            -webkit-background-clip: padding-box;
+            -moz-background-clip: padding-box;
+            background-clip: padding-box;
+        }
+
+        span.PhylovizCloseBtn{
+            cursor: pointer;
+            float : right;
+        }
+
+        #PhyloViz{
+            width: 100%;
+            height: 95%;
+        }
+
+        h2.PhyloVizMenuTitle{
+            color: white;
+        }
+
+        ##        Settings Menu
+        .SettingMenuRows{
+                    margin: 2px 0 2px 0;
+                }
+
+
+        ##        Helper Styles
+        .PhyloVizFloatLeft{
+                    float : left;
+                }
+        .icon-button.zoom-in,.icon-button.zoom-out{display:inline-block;he=
ight:16px;width:16px;margin-bottom:-3px;cursor:pointer;}
+        .icon-button.zoom-out{background:transparent url(../images/fugue/m=
agnifier-zoom-out.png) center center no-repeat;}
+        .icon-button.zoom-in{margin-left:10px;background:transparent url(.=
./images/fugue/magnifier-zoom.png) center center no-repeat;}
+
+    </style>
+</%def>
+
+
+<%def name=3D"javascripts()">
+    ${parent.javascripts()}
+    ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "=
viz/phyloviz")}
+</%def>
+
+
+
+<%def name=3D"center_panel()">
+
+    <div class=3D"unified-panel-header" unselectable=3D"on">
+        <div class=3D"unified-panel-header-inner">
+            <div style=3D"float:left;" id=3D"title"></div>
+            <div style=3D"float:right;" id=3D"panelHeaderRightBtns"></div>
+        </div>
+        <div style=3D"clear: both"></div>
+    </div>
+
+
+    <div id=3D"phyloVizNavContainer">
+        <div id=3D"phyloVizNav">
+            %if config["ext"] =3D=3D "nex" and not config["saved_visualiza=
tion"]:
+                <div id =3D "phylovizNexInfo" class=3D"navControl">
+                <p>Select a tree to view:   
+                <select id=3D"phylovizNexSelector">
+                    % for tree, index in config["trees"]:
+                        <option value=3D"${index}">${tree}</option>
+                    % endfor
+                </select>
+                </p>
+                </div>
+            %endif
+            <div id=3D"phyloVizNavBtns" class=3D"navControl">
+            </div>
+            <div class=3D"navControl">
+                <p> | Alt+click to select nodes</p>
+            </div>
+
+
+        </div>
+
+    </div>
+
+    ##  Node Selection Menu
+    <div id=3D"nodeSelectionView" class=3D"Panel">
+        <div class=3D"modal-header">
+            <h3 class=3D"PhyloVizMenuTitle">Search / Edit Nodes :
+                <span class=3D"PhylovizCloseBtn" id=3D"nodeSelCloseBtn"> X=
 </span>
+            </h3>
+        </div>
+
+        <div class=3D"modal-body">
+
+            <div class=3D"SettingMenuRows">
+                Search for nodes with:
+                <select id=3D"phyloVizSearchCondition" style=3D"width: 55%=
">
+                    <option value=3D"name-containing">Name (containing)</o=
ption>
+                    <option value=3D"annotation-containing">Annotation (co=
ntaining)</option>
+                    <option value=3D"dist-greaterEqual">Distance (>=3D)</o=
ption>
+                    <option value=3D"dist-lesserEqual">Distance (<=3D)</op=
tion>
+                </select>
+                <input  type=3D"text" id=3D"phyloVizSearchTerm" value=3D"N=
one" size=3D"15" displayLabel=3D"Distance">
+
+                <div class=3D"SettingMenuRows" style=3D"text-align: center=
;">
+                    <button id=3D"phyloVizSearchBtn" > Search! </button>
+                </div>
+            </div>
+
+            <br/>
+
+            <div class=3D"SettingMenuRows">
+                Name: <input type=3D"text" id=3D"phyloVizSelectedNodeName"=
 value=3D"None" size=3D"15" disabled=3D"disabled" >
+            </div>
+            <div class=3D"SettingMenuRows">
+                Dist: <input type=3D"text" id=3D"phyloVizSelectedNodeDist"=
 value=3D"None" size=3D"15" disabled=3D"disabled" displayLabel=3D"Distance">
+            </div>
+            <div class=3D"SettingMenuRows">
+                Annotation:
+                <textarea id=3D"phyloVizSelectedNodeAnnotation" disabled=
=3D"disabled" ></textarea>
+            </div>
+            <div class=3D"SettingMenuRows">
+                Edit: <input type=3D"checkbox" id=3D"phylovizEditNodesChec=
k" value=3D"You can put custom annotations here and it will be saved">
+                <button id=3D"phylovizNodeSaveChanges" style=3D"display: n=
one;"> Save edits</button>
+                <button id=3D"phylovizNodeCancelChanges" style=3D"display:=
 none;"> Cancel</button>
+            </div>
+        </div>
+    </div>
+
+    ##  Settings Menus
+    <div id=3D"SettingsMenu" class=3D"Panel">
+        <div class=3D"modal-header">
+            <h3 class=3D"PhyloVizMenuTitle">Phyloviz Settings:
+                <span class=3D"PhylovizCloseBtn" id=3D"settingsCloseBtn"> =
X </span>
+            </h3>
+        </div>
+        <div class=3D"modal-body">
+            <div class=3D"SettingMenuRows">
+                Phylogenetic Spacing (px per unit): <input id=3D"phyloVizT=
reeSeparation" type=3D"text" value=3D"250" size=3D"10" displayLabel=3D"Phyl=
ogenetic Separation"> (50-2500)
+            </div>
+            <div class=3D"SettingMenuRows">
+                Vertical Spacing (px): <input type=3D"text" id=3D"phyloViz=
TreeLeafHeight" value=3D"18" size=3D"10" displayLabel=3D"Vertical Spacing">=
 (5-30)
+            </div>
+            <div class=3D"SettingMenuRows">
+                Font Size (px): <input type=3D"text" id=3D"phyloVizTreeFon=
tSize" value=3D"12" size=3D"4" displayLabel=3D"Font Size"> (5-20)
+            </div>
+
+        </div>
+        <div class=3D"modal-footer">
+            <button id=3D"phylovizResetSettingsBtn" class=3D"PhyloVizFloat=
Left" > Reset </button>
+            <button id=3D"phylovizApplySettingsBtn" class=3D"PhyloVizFloat=
Right" > Apply </button>
+        </div>
+    </div>
+
+
+
+
+
+
+    <div class=3D"Panel" id=3D"FloatingMenu" style=3D"display: None;">
+
+        <h2>PhyloViz (<a onclick=3D"displayHelp()" href=3D"javascript:void=
(0);">?</a>)</h2>
+        <div style=3D"display: none;">
+            <h2>Summary of Interactions and Functions:</h2>
+            <div class=3D"hint">1. Expansion of Nodes: click or option-cli=
ck to expand or collapse</div>
+            <div class=3D"hint">2. Zooming and translation: mousewheel, bu=
ttons, click and drag, double click. Reset</div>
+            <div class=3D"hint">3. Tooltip: Displays "Name and Size" on mo=
useOver on nodes</div>
+            <div class=3D"hint">4. Minimap: Currently displays an exact bu=
t scaled down replicate of the tree, orange bounding box is correct for lin=
ear only<br/>
+                Can be switched on or off</div>
+            <div class=3D"hint">5. Changing Layouts: Able to change betwee=
n circular and linear layouts.</div>
+
+        </div>
+
+        <h5>Scaling & Rotation:</h5>
+        <button id=3D"phylovizZoomInBtn" class=3D"" > + </button>
+        <button id=3D"phylovizZoomOutBtn" class=3D"" > - </button>
+
+
+        <h5>Translation:</h5>
+        <button id=3D"phylovizTranslateUpBtn" > Up </button>
+        <button id=3D"phylovizTranslateDownBtn" > Down </button>
+        <br/>
+        <button id=3D"phylovizTranslateLeftBtn" > Left </button>
+        <button id=3D"phylovizTranslateRightBtn" > Right </button>
+
+
+
+        <h5>Others:</h5>
+        <button id=3D"phylovizResetBtn" > Reset Zoom/Translate </button>
+        <button id=3D"phylovizSaveBtn" > Save vizualization </button>
+        <button id=3D"phylovizOpenSettingsBtn" > Settings </button>
+    </div>
+
+    <div id=3D"PhyloViz" >
+    </div>
+
+    <script type=3D"text/javascript">
+
+        function initPhyloViz(data, config) {
+            var phyloviz;
+
+            // -- Initialization code |-->
+            phyloviz =3D new PhylovizView({
+                data: data,
+                layout : "Linear",
+                config :  config
+            });
+
+            // -- Render viz. --
+            phyloviz.render();
+
+        }
+
+        $(function firstVizLoad(){       // calls when viz is loaded for t=
he first time
+            var config =3D JSON.parse( '${ h.to_json_string( config )}');
+            var data =3D JSON.parse('${h.to_json_string(data)}');
+            initPhyloViz(data, config);
+        });
+
+    </script>
+
+</%def>
+
+


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 test-data/visualization/phyloviz/1_nexus.nex
--- /dev/null
+++ b/test-data/visualization/phyloviz/1_nexus.nex
@@ -0,0 +1,87 @@
+#NEXUS
+
+[!This data set was downloaded from TreeBASE, a relational database of phy=
logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer=
sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl=
edgment from the Nexus file.
+
+
+Generated on June 12, 2012; 23:00 GMT
+
+TreeBASE (cc) 1994-2008
+
+Study reference:
+Olariaga I., Grebenc T., Salcedo I., & Mart=C3=ADn M.P. 2012. Two new spec=
ies of Hydnum
+with ovoid basidiospores: H. ovoideisporum and H. vesterholtii. Mycologia,=
 .
+
+TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S128=
31]
+
+BEGIN TREES;
+      TITLE Hydnum_ITS_result;
+      LINK TAXA =3D Taxa1;
+         TRANSLATE
+            1    Hydnum_aff_ellipsosporum_RUFHYD1_AJ535304,
+            2    Hydnum_albidum_ALB_AY817135,
+            3    Hydnum_albidum_ALBHYD1_AJ534974,
+            4    Hydnum_albomagnum_ALM_DQ218305,
+            5    Hydnum_ellipsosporum_ELL_AY817138,
+            6    Hydnum_ellipsosporum_RUFHYD8_AJ547882,
+            7    Hydnum_ovoidisporum_12317BIOFungi,
+            8    Hydnum_ovoidisporum_12683BIOFungi,
+            9    Hydnum_ovoidisporum_12902BIOFungi,
+            10   Hydnum_ovoidisporum_14130BIOFungi,
+            11   Hydnum_repandum_RE1_REP1_AJ889978,
+            12   Hydnum_repandum_RE1_REP2_AJ889949,
+            13   Hydnum_repandum_RE1_REP3_AY817136,
+            14   Hydnum_repandum_RE1_REP6_UDB000025,
+            15   Hydnum_repandum_RE1_REP7_UDB000096,
+            16   Hydnum_repandum_RE1_REP8_UDB001479,
+            17   Hydnum_repandum_RE1_REPHYD10_AJ547888,
+            18   Hydnum_repandum_RE1_REPHYD11_AJ547886,
+            19   Hydnum_repandum_RE1_REPHYD1_AJ547871,
+            20   Hydnum_repandum_RE1_REPHYD3_AJ547874,
+            21   Hydnum_repandum_RE1_REPHYD4_AJ547876,
+            22   Hydnum_repandum_RE1_REPHYD5_AJ547875,
+            23   Hydnum_repandum_RE1_REPHYD6_AJ547877,
+            24   Hydnum_repandum_RE1_REPHYD7_AJ547878,
+            25   Hydnum_repandum_RE1_REPHYD8_AJ547881,
+            26   Hydnum_repandum_RE1_REPHYD9_AJ547883,
+            27   Hydnum_repandum_RE1_RUFHYD10_AJ547866,
+            28   Hydnum_repandum_RE1_RUFHYD11_AJ547889,
+            29   Hydnum_repandum_RE1_RUFHYD9_AJ535305,
+            30   Hydnum_rufescens_RU1_RUFHYD5_AJ547869,
+            31   Hydnum_rufescens_RU1_RUFHYD6_AJ547884,
+            32   Hydnum_rufescens_RU1_RUFHYD7_AJ547870,
+            33   Hydnum_rufescens_RU2_REP5_DQ367902,
+            34   Hydnum_rufescens_RU2_RUFHYD2_AJ535301,
+            35   Hydnum_rufescens_RU3_12901BIOFungi,
+            36   Hydnum_rufescens_RU3_REP4_DQ218306,
+            37   Hydnum_rufescens_RU3_RUFHYD3_AJ535303,
+            38   Hydnum_rufescens_RU3_RUFHYD4_AJ535302,
+            39   Hydnum_rufescens_RU4_RUFHYD12_AJ839969,
+            40   Hydnum_rufescens_RU4_RUFHYD16_AJ547868,
+            41   Hydnum_rufescens_RU4_RUFHYD17_AJ547885,
+            42   Hydnum_rufescens_RU4_UMB1_DQ367903,
+            43   Hydnum_rufescens_RU5_12760BIOFungi,
+            44   Hydnum_rufescens_RU5_ALBHYD2_AJ534975,
+            45   Hydnum_rufescens_RU5_RUF2_DQ658890,
+            46   Hydnum_rufescens_RU5_RUF4_UDB001465,
+            47   Hydnum_rufescens_RU5_RUF5_UDB002423,
+            48   Hydnum_rufescens_RU5_RUFHYD14_AJ547872,
+            49   Hydnum_rufescens_RU6_RUF1_AY817137,
+            50   Hydnum_rufescens_RU6_RUFHYD15_AJ547867,
+            51   Hydnum_rufescens_wrong_taxonomy_RUF3_AM087246,
+            52   Hydnum_umbilicatum_UMBHYD1_AJ534972,
+            53   Hydnum_umbilicatum_UMBHYD2_AJ534973,
+            54   Hydnum_vesterholtii_10429BIOFungi,
+            55   Hydnum_vesterholtii_10452BIOFungi,
+            56   Hydnum_vesterholtii_12330BIOFungi,
+            57   Hydnum_vesterholtii_12904BIOFungi,
+            58   Hydnum_vesterholtii_REPHYD12A_AJ547879,
+            59   Hydnum_vesterholtii_REPHYD12C_AJ783968,
+            60   Hydnum_vesterholtii_REPHYD13_AJ547887,
+            61   Sistotrema_muscicola_AJ606040,
+            62   Sistotrema_alboluteum_AJ606042;
+      TREE Fig._2 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66=
,((4:100.0,(2:100.0,3:100.0):100.0):60.639999,(((56:100.0,58:100.0,59:100.0=
):84.639999,(54:100.0,55:100.0,57:100.0,60:100.0):98.330002):92.5,(((30:100=
.0,31:100.0,32:100.0):100.0,(11:100.0,12:100.0,13:100.0,14:100.0,15:100.0,1=
6:100.0,17:100.0,18:100.0,19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,24:1=
00.0,25:100.0,26:100.0):99.93):68.690002,(((33:100.0,34:100.0):49.8050005,(=
35:100.0,36:100.0,37:100.0,38:100.0):99.989998):49.8050005,((7:100.0,8:100.=
0,9:100.0,10:100.0):100.0,(42:100.0,(39:100.0,40:100.0,41:100.0):98.449997)=
:86.790001,((52:100.0,53:100.0):99.93,(1:100.0,(5:97.47999949999999,6:100.0=
):97.47999949999999):100.0):53.310001,(27:100.0,(28:100.0,29:100.0,49:100.0=
,50:100.0):47.404999):47.404999,(43:100.0,44:100.0,45:100.0,46:100.0,47:100=
.0,48:100.0):99.459999):29.245001):29.245001):51.580002):61.540001):49.66);
+      TREE PAUP_1 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66=
,((4:100.0,(3:100.0,2:100.0):100.0):60.639999,(((58:100.0,59:100.0,56:100.0=
):84.639999,(60:100.0,54:100.0,55:100.0,57:100.0):98.330002):92.5,(((30:100=
.0,31:100.0,32:100.0):100.0,(19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,2=
4:100.0,25:100.0,26:100.0,17:100.0,18:100.0,11:100.0,12:100.0,13:100.0,14:1=
00.0,15:100.0,16:100.0):99.93):68.690002,((34:100.0,33:100.0):99.610001,(37=
:100.0,38:100.0,35:100.0,36:100.0):99.989998,(42:100.0,(39:100.0,41:100.0,4=
0:100.0):98.449997):86.790001,(8:100.0,7:100.0,9:100.0,10:100.0):100.0,((52=
:100.0,53:100.0):99.93,(1:100.0,(5:100.0,6:100.0):94.959999):100.0):53.3100=
01,(29:100.0,27:100.0,28:100.0,50:100.0,49:100.0):94.809998,(44:100.0,43:10=
0.0,48:100.0,45:100.0,46:100.0,47:100.0):99.459999):58.490002):51.580002):6=
1.540001):49.66);
+
+
+
+END;


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 test-data/visualization/phyloviz/2_nexus.nex
--- /dev/null
+++ b/test-data/visualization/phyloviz/2_nexus.nex
@@ -0,0 +1,96 @@
+#NEXUS
+
+[!This data set was downloaded from TreeBASE, a relational database of phy=
logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer=
sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl=
edgment from the Nexus file.
+
+
+Generated on August 18, 2012; 12:14 GMT
+
+TreeBASE (cc) 1994-2008
+
+Study reference:
+Naish D., Dyke G., Cau A., & Escuilli=C3=A9 F. 2012. A gigantic bird from =
the Upper Cretaceous
+of Central Asia. Biology Letters, 8(1): 97-100.
+
+TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S130=
08]
+
+BEGIN TREES;
+      TITLE Imported_trees;
+      LINK TAXA =3D Taxa1;
+         TRANSLATE
+            1    Herrerasaurus,
+            2    Tawa,
+            3    Allosaurus,
+            4    Alvarezsaurus,
+            5    Anchiornis,
+            6    Archaeopteryx,
+            7    Archaeorhynchus,
+            8    Avimimus,
+            9    Baryonyx,
+            10   Beipiaosaurus,
+            11   Caenagnathus,
+            12   Caudipteryx,
+            13   Ceratosaurus,
+            14   Chirostenotes,
+            15   Citipati,
+            16   Compsognathus,
+            17   Confuciusornis,
+            18   Dilong,
+            19   Dilophosaurus,
+            20   Epidendrosaurus,
+            21   Epidexipteryx,
+            22   Erlicosaurus,
+            23   Eustreptospondylus,
+            24   Gallimimus,
+            25   Garudimimus,
+            26   Gobipteryx,
+            27   Guanlong,
+            28   Haplocheirus,
+            29   Harpymimus,
+            30   Hebeiornis,
+            31   Hongshanornis,
+            32   Huoshanornis,
+            33   Iberomesornis,
+            34   Ichthyornis,
+            35   Incisivosaurus,
+            36   Jeholornis,
+            37   Limusaurus,
+            38   Longicrusavis,
+            39   Longipteryx,
+            40   Longirostravis,
+            41   Majungasaurus,
+            42   Masiakasaurus,
+            43   Monolophosaurus,
+            44   Mononykus,
+            45   Neornithes,
+            46   Ornitholestes,
+            47   Ornithomimus,
+            48   Patagonykus,
+            49   Patagopteryx,
+            50   Pelecanimimus,
+            51   Pengornis,
+            52   Protarchaeopteryx,
+            53   Protopteryx,
+            54   Rinchenia,
+            55   Sapeornis,
+            56   Segnosaurus,
+            57   Shenzhousaurus,
+            58   Shuvuuia,
+            59   Sinornithosaurus,
+            60   Sinosauropteryx,
+            61   Sinovenator,
+            62   Sinraptor,
+            63   Syntarsus_kayentakatae,
+            64   Troodon,
+            65   Tyrannosaurus,
+            66   Velociraptor,
+            67   Yanornis,
+            68   Yixianornis,
+            69   Zhongjianornis,
+            70   Zhongornis,
+            71   Zuolong,
+            72   Samrukia;
+      TREE Figure_1A =3D [&R] (1,(2,(((((43,(3,62)),(71,((46,((((28,(4,(48=
,(44,58)))),((((5,(61,(64,(59,66)))),(6,((36,(55,(69,(((7,34,45,49,72,(31,3=
8),(67,68)),(33,((32,((26,30),(39,40))),(51,53)))),(17,70))))),(20,21)))),(=
(11,(12,(8,(14,(15,54))))),(35,52))),(10,(22,56)))),(50,(57,(29,(25,(24,47)=
))))),(16,60))),(27,(18,65))))),(9,23)),(13,(41,(37,42)))),(19,63))));
+
+
+
+END;


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 test-data/visualization/phyloviz/3_phyloxml.xml
--- /dev/null
+++ b/test-data/visualization/phyloviz/3_phyloxml.xml
@@ -0,0 +1,257 @@
+<?xml version=3D"1.0" encoding=3D"UTF-8"?>
+<phyloxml xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance"
+   xsi:schemaLocation=3D"http://www.phyloxml.org http://www.phyloxml.org/1=
.10/phyloxml.xsd"
+   xmlns=3D"http://www.phyloxml.org">
+   <phylogeny rooted=3D"true">
+      <clade>
+         <clade>
+            <branch_length>0.18105</branch_length>
+            <confidence type=3D"unknown">89.0</confidence>
+            <clade>
+               <branch_length>0.07466</branch_length>
+               <confidence type=3D"unknown">32.0</confidence>
+               <clade>
+                  <branch_length>0.26168</branch_length>
+                  <confidence type=3D"unknown">100.0</confidence>
+                  <clade>
+                     <branch_length>0.22058</branch_length>
+                     <confidence type=3D"unknown">89.0</confidence>
+                     <clade>
+                        <branch_length>0.28901</branch_length>
+                        <confidence type=3D"unknown">100.0</confidence>
+                        <clade>
+                           <branch_length>0.06584</branch_length>
+                           <confidence type=3D"unknown">100.0</confidence>
+                           <clade>
+                              <branch_length>0.02309</branch_length>
+                              <confidence type=3D"unknown">43.0</confidenc=
e>
+                              <clade>
+                                 <branch_length>0.0746</branch_length>
+                                 <confidence type=3D"unknown">100.0</confi=
dence>
+                                 <clade>
+                                    <branch_length>0.02365</branch_length>
+                                    <confidence type=3D"unknown">88.0</con=
fidence>
+                                    <clade>
+                                       <name>22_MOUSE</name>
+                                       <branch_length>0.05998</branch_leng=
th>
+                                       <taxonomy>
+                                          <code>MOUSE</code>
+                                       </taxonomy>
+                                    </clade>
+                                    <clade>
+                                       <name>Apaf-1_HUMAN</name>
+                                       <branch_length>0.01825</branch_leng=
th>
+                                       <taxonomy>
+                                          <code>HUMAN</code>
+                                       </taxonomy>
+                                    </clade>
+                                 </clade>
+                                 <clade>
+                                    <name>12_CANFA</name>
+                                    <branch_length>0.04683</branch_length>
+                                    <taxonomy>
+                                       <code>CANFA</code>
+                                    </taxonomy>
+                                 </clade>
+                              </clade>
+                              <clade>
+                                 <name>11_CHICK</name>
+                                 <branch_length>0.15226</branch_length>
+                                 <taxonomy>
+                                    <code>CHICK</code>
+                                 </taxonomy>
+                              </clade>
+                           </clade>
+                           <clade>
+                              <name>16_XENLA</name>
+                              <branch_length>0.4409</branch_length>
+                              <taxonomy>
+                                 <code>XENLA</code>
+                              </taxonomy>
+                           </clade>
+                        </clade>
+                        <clade>
+                           <branch_length>0.17031</branch_length>
+                           <confidence type=3D"unknown">100.0</confidence>
+                           <clade>
+                              <branch_length>0.10929</branch_length>
+                              <confidence type=3D"unknown">100.0</confiden=
ce>
+                              <clade>
+                                 <name>14_FUGRU</name>
+                                 <branch_length>0.02255</branch_length>
+                                 <taxonomy>
+                                    <code>FUGRU</code>
+                                 </taxonomy>
+                              </clade>
+                              <clade>
+                                 <name>15_TETNG</name>
+                                 <branch_length>0.09478</branch_length>
+                                 <taxonomy>
+                                    <code>TETNG</code>
+                                 </taxonomy>
+                              </clade>
+                           </clade>
+                           <clade>
+                              <name>17_BRARE</name>
+                              <branch_length>0.1811</branch_length>
+                              <taxonomy>
+                                 <code>BRARE</code>
+                              </taxonomy>
+                           </clade>
+                        </clade>
+                     </clade>
+                     <clade>
+                        <branch_length>0.01594</branch_length>
+                        <confidence type=3D"unknown">53.0</confidence>
+                        <clade>
+                           <branch_length>0.10709</branch_length>
+                           <confidence type=3D"unknown">68.0</confidence>
+                           <clade>
+                              <name>1_BRAFL</name>
+                              <branch_length>0.26131</branch_length>
+                              <taxonomy>
+                                 <code>BRAFL</code>
+                              </taxonomy>
+                           </clade>
+                           <clade>
+                              <name>18_NEMVE</name>
+                              <branch_length>0.38014</branch_length>
+                              <taxonomy>
+                                 <code>NEMVE</code>
+                              </taxonomy>
+                           </clade>
+                        </clade>
+                        <clade>
+                           <name>23_STRPU</name>
+                           <branch_length>0.48179</branch_length>
+                           <taxonomy>
+                              <code>STRPU</code>
+                           </taxonomy>
+                        </clade>
+                     </clade>
+                  </clade>
+                  <clade>
+                     <branch_length>0.34475</branch_length>
+                     <confidence type=3D"unknown">100.0</confidence>
+                     <clade>
+                        <name>26_STRPU</name>
+                        <branch_length>0.36374</branch_length>
+                        <taxonomy>
+                           <code>STRPU</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"1319">
+                              <domain from=3D"18" to=3D"98" confidence=3D"=
3.4E-5">Death</domain>
+                              <domain from=3D"189" to=3D"481" confidence=
=3D"1.8E-10">NB-ARC</domain>
+                              <domain from=3D"630" to=3D"668" confidence=
=3D"8.2E-5">WD40</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                     <clade>
+                        <name>25_STRPU</name>
+                        <branch_length>0.33137</branch_length>
+                        <taxonomy>
+                           <code>STRPU</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"1947">
+                              <domain from=3D"143" to=3D"227" confidence=
=3D"7.4E-5">Death</domain>
+                              <domain from=3D"227" to=3D"550" confidence=
=3D"2.0E-13">NB-ARC</domain>
+                              <domain from=3D"697" to=3D"736" confidence=
=3D"7.9E-4">WD40</domain>
+                              <domain from=3D"745" to=3D"785" confidence=
=3D"1.5">WD40</domain>
+                              <domain from=3D"1741" to=3D"1836" confidence=
=3D"2.0">Adeno_VII</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+               </clade>
+               <clade>
+                  <branch_length>1.31498</branch_length>
+                  <confidence type=3D"unknown">100.0</confidence>
+                  <clade>
+                     <name>CED4_CAEEL</name>
+                     <branch_length>0.13241</branch_length>
+                     <taxonomy>
+                        <code>CAEEL</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length=3D"714">
+                           <domain from=3D"7" to=3D"90" confidence=3D"9.2E=
-14">CARD</domain>
+                           <domain from=3D"116" to=3D"442" confidence=3D"5=
.8E-151">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+                  <clade>
+                     <name>31_CAEBR</name>
+                     <branch_length>0.04777</branch_length>
+                     <taxonomy>
+                        <code>CAEBR</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length=3D"554">
+                           <domain from=3D"1" to=3D"75" confidence=3D"0.00=
46">CARD</domain>
+                           <domain from=3D"101" to=3D"427" confidence=3D"2=
.1E-123">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+            </clade>
+            <clade>
+               <branch_length>0.13172</branch_length>
+               <confidence type=3D"unknown">45.0</confidence>
+               <clade>
+                  <branch_length>0.24915</branch_length>
+                  <confidence type=3D"unknown">95.0</confidence>
+                  <clade>
+                     <branch_length>0.76898</branch_length>
+                     <confidence type=3D"unknown">100.0</confidence>
+                     <clade>
+                        <name>28_DROPS</name>
+                        <branch_length>0.1732</branch_length>
+                        <taxonomy>
+                           <code>DROPS</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"535">
+                              <domain from=3D"112" to=3D"399" confidence=
=3D"1.4E-5">NB-ARC</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                     <clade>
+                        <name>Dark_DROME</name>
+                        <branch_length>0.18863</branch_length>
+                        <taxonomy>
+                           <code>DROME</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"1421">
+                              <domain from=3D"108" to=3D"397" confidence=
=3D"2.1E-5">NB-ARC</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+                  <clade>
+                     <name>29_AEDAE</name>
+                     <branch_length>0.86398</branch_length>
+                     <taxonomy>
+                        <code>AEDAE</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length=3D"423">
+                           <domain from=3D"109" to=3D"421" confidence=3D"9=
.3E-6">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+               <clade>
+                  <name>30_TRICA</name>
+                  <branch_length>0.97698</branch_length>
+                  <taxonomy>
+                     <code>TRICA</code>
+                  </taxonomy>
+               </clade>
+            </clade>
+         </clade>
+      </clade>
+   </phylogeny>
+</phyloxml>


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 test-data/visualization/phyloviz/4_newick.nhx
--- /dev/null
+++ b/test-data/visualization/phyloviz/4_newick.nhx
@@ -0,0 +1,33 @@
+(((BGIOSIBCA028421_ORYSA:0.423485[&&NHX:S=3DORYSA:O=3DBGIOSIBCA028421.1:G=
=3DBGIOSIBCA028421],
+At5g41150_ARATH:0.273135[&&NHX:S=3DARATH:O=3DAt5g41150.1:G=3DAt5g41150]
+):0.690991[&&NHX:S=3DMagnoliophyta:D=3DN:B=3D100],
+(rad16_SCHPO:0.718598[&&NHX:S=3DSCHPO:O=3DSPCC970.01:G=3DSPCC970.01],
+RAD1_YEAST:1.05456[&&NHX:S=3DYEAST:O=3DYPL022W.1:G=3DYPL022W]
+):0.344838[&&NHX:S=3DAscomycota:D=3DN:B=3D100]
+):0.103849[&&NHX:S=3DEukaryota:D=3DN:B=3D61],
+((((((((ERCC4_HUMAN:0.067531[&&NHX:S=3DHUMAN:O=3DENST00000311895.3:G=3DENS=
G00000175595],
+Ercc4_MOUSE:0.17422[&&NHX:S=3DMOUSE:O=3DENSMUST00000023206.5:G=3DENSMUSG00=
000022545]
+):0.065513[&&NHX:S=3DEuarchontoglires:D=3DN:B=3D100],
+ENSMODT00000006086_MONDO:0.104633[&&NHX:S=3DMONDO:O=3DENSMODT00000006086.2=
:G=3DENSMODG00000004840]
+):0.083764[&&NHX:S=3DTheria:D=3DN:B=3D100],
+Q5ZJP8_CHICK:0.153132[&&NHX:S=3DCHICK:O=3DENSGALT00000004716.2:G=3DENSGALG=
00000002981]
+):0.057998[&&NHX:S=3DAmniota:D=3DN:B=3D100],
+ENSXETT00000024054_XENTR:0.288632[&&NHX:S=3DXENTR:O=3DENSXETT00000024054.2=
:G=3DENSXETG00000010991]
+):0.075713[&&NHX:S=3DTetrapoda:D=3DN:B=3D100],
+(zgc-63468_BRARE:0.2218[&&NHX:S=3DBRARE:O=3DENSDART00000015780.4:G=3DENSDA=
RG00000014161],
+NEWSINFRUT00000137921_FUGRU:0.220441[&&NHX:S=3DFUGRU:O=3DNEWSINFRUT0000013=
7921.3:G=3DNEWSINFRUG00000130312]
+):0.170605[&&NHX:S=3DClupeocephala:D=3DN:B=3D100]
+):0.238713[&&NHX:S=3DEuteleostomi:D=3DN:B=3D100],
+ENSCINT00000011737_CIOIN:0.623567[&&NHX:S=3DCIOIN:O=3DENSCINT00000011737.2=
:G=3DENSCING00000005673]
+):0.07499[&&NHX:S=3DChordata:D=3DN:B=3D100],
+(Sm00.scaff00195.0600_SCHMA:0.784609[&&NHX:S=3DSCHMA:O=3DSm00.scaff00195.0=
600:G=3DSm00.scaff00195.0600],
+(CBG03141_CAEBR:0.093703[&&NHX:S=3DCAEBR:O=3DCBG03141:G=3DCBG03141],
+NP_496498_CAEEL:0.212236[&&NHX:S=3DCAEEL:O=3DC47D12.8.1:G=3DC47D12.8]
+):1.47416[&&NHX:S=3DCaenorhabditis:D=3DN:B=3D94]
+):0.26906[&&NHX:S=3DBilateria:D=3DN:B=3D97]
+):0.071406[&&NHX:S=3DBilateria:D=3DN:B=3D1],
+(mei-9-RA_DROME:0.170289[&&NHX:S=3DDROME:O=3DCG3697-RA.3:G=3DCG3697],
+GA17620-PA_DROPS:0.154817[&&NHX:S=3DDROPS:O=3DGA17620-PA:G=3DGA17620]
+):0.818474[&&NHX:S=3DSophophora:D=3DN:B=3D100]
+):0
+)[&&NHX:S=3DEukaryota:D=3DN];
\ No newline at end of file


diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba=
ffb65374729d51b89 test-data/visualization/phyloviz/5_newick.nhx
--- /dev/null
+++ b/test-data/visualization/phyloviz/5_newick.nhx
@@ -0,0 +1,1 @@
+(CAE_ELE_PORCN:0.303421 ,((((DRO_PER_PORCN:0.001000 ,DRO_PSE_PORCN:0.00100=
0 )67:0.141994 ,(DRO_ANA_PORCN:0.111899 ,(DRO_ERE_PORCN:0.030516 ,(DRO_MEL_=
PORCN:0.021127 ,DRO_SEC_PORCN:0.021127 )38:0.030516 )35:0.111899 )18:0.1419=
94 )16:0.162611 ,(DRO_WIL_PORCN:0.152225 ,(DRO_VIR_PORCN:0.085057 ,DRO_MOJ_=
PORCN:0.085057 )24:0.152225 )15:0.162611 )13:0.295081 ,(ANO_GAM_PORCN:0.287=
545 ,((CIO_INT_PORCN:0.100686 ,CIO_SAV_PORCN:0.100686 )19:0.275542 ,((LOA_L=
OA_PORCN:0.036278 ,BRU_MAL_PORCN:0.036278 )29:0.272631 ,(((((DAN_RER_PORCN:=
0.086499 ,((TAK_RUB_PORCN:0.032609 ,TET_NIG_PORCN:0.032609 )32:0.048864 ,(G=
AD_MOR_PORCN:0.039387 ,(ORY_LAT_PORCN:0.031729 ,(GAS_ACU_PORCN:0.021882 ,OR=
E_NIL_PORCN:0.021882 )37:0.031729 )34:0.039387 )28:0.048864 )27:0.086499 )2=
3:0.119618 ,(LAT_CHA_PORCN:0.099348 ,((XEN_LAE_PORCN:0.033333 ,XEN_TRO_PORC=
N:0.033333 )31:0.091250 ,(ANO_CAR_PORCN:0.086538 ,((MON_DOM_PORCN:0.014100 =
,(MAC_EUG_PORCN:0.005423 ,SAR_HAR_PORCN:0.005423 )57:0.014100 )42:0.062862 =
,(ORN_ANA_PORCN:0.057974 ,(GOR_GOR_PORCN:0.033876 ,(FEL_CAT_PORCN:0.022851 =
,(PRO_CAP_PORCN:0.019716 ,(CAV_POR_PORCN:0.018599 ,(ERI_EUR_PORCN:0.015518 =
,((DIP_ORD_PORCN:0.007231 ,(MUS_MUS_PORCN:0.001085 ,(RAT_NOR_PORCN:0.001000=
 ,CRI_GRI_PORCN:0.001000 )69:0.001085 )64:0.007231 )53:0.012954 ,(DAS_NOV_P=
ORCN:0.011362 ,(LOX_AFR_PORCN:0.010575 ,(CAL_JAC_PORCN:0.010332 ,(OCH_PRI_P=
ORCN:0.010063 ,(MIC_MUR_PORCN:0.009123 ,(SUS_SCR_PORCN:0.008880 ,(MYO_LUC_P=
ORCN:0.008460 ,((CAN_FAM_PORCN:0.005423 ,AIL_MEL_PORCN:0.005423 )58:0.00809=
3 ,((PTE_VAM_PORCN:0.006508 ,BOS_TAU_PORCN:0.006508 )55:0.007494 ,((SPE_TRI=
_PORCN:0.003254 ,TUP_BEL_PORCN:0.003254 )61:0.006929 ,((OTO_GAR_PORCN:0.001=
085 ,(ORY_CUN_PORCN:0.001000 ,TUR_TRU_PORCN:0.001000 )68:0.001085 )65:0.005=
965 ,(EQU_CAB_PORCN:0.003688 ,(MAC_MUL_PORCN:0.002711 ,(PAN_TRO_PORCN:0.001=
446 ,(HOM_SAP_PORCN:0.001085 ,(PON_ABE_PORCN:0.001000 ,NOM_LEU_PORCN:0.0010=
00 )70:0.001085 )66:0.001446 )63:0.002711 )62:0.003688 )60:0.005965 )56:0.0=
06929 )54:0.007494 )52:0.008093 )51:0.008460 )50:0.008880 )49:0.009123 )48:=
0.010063 )47:0.010332 )46:0.010575 )45:0.011362 )44:0.012954 )43:0.015518 )=
41:0.018599 )40:0.019716 )39:0.022851 )36:0.033876 )30:0.057974 )26:0.06286=
2 )25:0.086538 )22:0.091250 )21:0.099348 )20:0.119618 )17:0.214465 ,(BRA_FL=
O_PORCN:0.189220 ,SAC_KOW_PORCN:0.189220 )12:0.214465 )11:0.257058 ,(NEM_VE=
C_PORCN:0.246631 ,AMP_QUE_PORCN:0.246631 )9:0.257058 )8:0.266904 ,(TRI_CAS_=
PORCN:0.259494 ,(PED_HUM_PORCN:0.227009 ,(NAS_VIT_PORCN:0.160241 ,(API_MEL_=
PORCN:0.031851 ,(BOM_TER_PORCN:0.004808 ,BOM_IMP_PORCN:0.004808 )59:0.03185=
1 )33:0.160241 )14:0.227009 )10:0.259494 )7:0.266904 )6:0.272631 )5:0.27554=
2 )4:0.287545 )3:0.295081 )2:0.303421 )1:0.0001;



https://bitbucket.org/galaxy/galaxy-central/changeset/75a03bacdc7a/
changeset:   75a03bacdc7a
user:        jgoecks
date:        2012-08-27 20:08:55
summary:     Merged in Tomithy/galaxy-central-phyloviz-2 (pull request #65)
affected #:  19 files

diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -719,7 +719,49 @@
     pass
=20
 class Newick( Text ):
-    pass
+    """New Hampshire/Newick Format"""
+    file_ext =3D "nhx"
+
+    MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu=
mns", readonly=3DTrue )
+
+    def __init__(self, **kwd):
+        """Initialize foobar datatype"""
+        Text.__init__(self, **kwd)
+
+    def init_meta( self, dataset, copy_from=3DNone ):
+        Text.init_meta( self, dataset, copy_from=3Dcopy_from )
+
+
+    def sniff( self, filename ):
+        """ Returning false as the newick format is too general and cannot=
 be sniffed."""
+        return False
+
+
+class Nexus( Text ):
+    """Nexus format as used By Paup, Mr Bayes, etc"""
+    file_ext =3D "nex"
+
+    MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu=
mns", readonly=3DTrue )
+
+    def __init__(self, **kwd):
+        """Initialize foobar datatype"""
+        Text.__init__(self, **kwd)
+
+    def init_meta( self, dataset, copy_from=3DNone ):
+        Text.init_meta( self, dataset, copy_from=3Dcopy_from )
+
+
+    def sniff( self, filename ):
+        """All Nexus Files Simply puts a '#NEXUS' in its first line"""
+        f =3D open(filename, "r")
+        firstline =3D f.readline().upper()
+        f.close()
+
+        if "#NEXUS" in firstline:
+            return True
+        else:
+            return False
+
=20
 # ------------- Utility methods --------------
=20


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/datatypes/xml.py
--- a/lib/galaxy/datatypes/xml.py
+++ b/lib/galaxy/datatypes/xml.py
@@ -76,3 +76,24 @@
             dataset.blurb =3D 'file purged from disk'
     def sniff( self, filename ):
         return False
+
+class Phyloxml( GenericXml ):
+    """Format for defining phyloxml data http://www.phyloxml.org/"""
+    file_ext =3D "phyloxml"
+    def set_peek( self, dataset, is_multi_byte=3DFalse ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek =3D data.get_file_peek( dataset.file_name, is_mul=
ti_byte=3Dis_multi_byte )
+            dataset.blurb =3D 'Phyloxml data'
+        else:
+            dataset.peek =3D 'file does not exist'
+            dataset.blurb =3D 'file purged from disk'
+
+    def sniff( self, filename ):
+        """"Checking for keyword - 'phyloxml' always in lowercase in the f=
irst few lines"""
+        f =3D open(filename, "r")
+        firstlines =3D "".join(f.readlines(5))
+        f.close()
+        if "phyloxml" in firstlines:
+            return True
+        return False
\ No newline at end of file


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/visualization/phyloviz/__init__.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/__init__.py
@@ -0,0 +1,1 @@
+__author__ =3D 'Tomithy'


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/visualization/phyloviz/baseparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/baseparser.py
@@ -0,0 +1,125 @@
+import json
+
+class Node(object):
+    """Node class of PhyloTree, which represents a CLAUDE in a phylogeneti=
c tree"""
+    def __init__(self, nodeName, **kwargs):
+        """Creates a node and adds in the typical annotations"""
+        self.name, self.id =3D nodeName, kwargs.get("id", 0)
+        self.depth =3D kwargs.get("depth", 0)
+        self.children =3D []
+
+        self.isInternal =3D kwargs.get("isInternal", 0)
+        self.length, self.bootstrap =3D kwargs.get("length", 0), kwargs.ge=
t("bootstrap", None)
+        self.events =3D kwargs.get("events", "")
+
+        # clean up boot strap values
+        if self.bootstrap =3D=3D -1:
+            self.bootstrap =3D None
+
+    def addChildNode(self, child):
+        """Adds a child node to the current node"""
+        if isinstance(child, Node):
+            self.children.append(child)
+        else:
+            self.children +=3D child
+
+
+    def __str__(self):
+        return self.name + " id:" + str(self.id) + ", depth: " + str(self.=
depth)
+
+
+    def toJson(self):
+        """Converts the data in the node to a dict representation of json"=
""
+        thisJson =3D {
+            "name"      : self.name,
+            "id"        : self.id,
+            "depth"     : self.depth,
+            "dist"      : self.length
+        }
+        thisJson =3D self.addChildrenToJson(thisJson)
+        thisJson =3D self.addMiscToJson(thisJson)
+        return thisJson
+
+    def addChildrenToJson(self, jsonDict):
+        """Needs a special method to addChildren, such that the key does n=
ot appear in the Jsondict when the children is empty
+        this requirement is due to the layout algorithm used by d3 layout =
for hiding subtree """
+        if len(self.children) > 0:
+            children =3D [ node.toJson() for node in self.children]
+            jsonDict["children"] =3D children
+        return jsonDict
+
+
+    def addMiscToJson(self, jsonDict):
+        """Adds other misc attributes to json if they are present"""
+        if not self.events =3D=3D "":
+            jsonDict["events"] =3D self.events
+        if not self.bootstrap =3D=3D None:
+            jsonDict["bootstrap"] =3D self.bootstrap
+        return jsonDict
+
+
+
+class PhyloTree(object):
+    """Standardized python based class to represent the phylogenetic tree =
parsed from different
+    phylogenetic file formats."""
+
+    def __init__(self):
+        self.root, self.rootAttr =3D None, {}
+        self.nodes =3D {}
+        self.title =3D None
+        self.id =3D 1
+
+    def addAttributesToRoot(self, attrDict):
+        """Adds attributes to root, but first we put it in a temp store an=
d bind it with root when .toJson is called"""
+        for key, value in attrDict.items():
+            self.rootAttr[key] =3D value
+
+    def makeNode(self, nodeName, **kwargs):
+        """Called to make a node within PhyloTree, arbitrary kwargs can be=
 passed to annotate nodes
+        Tracks the number of nodes via internally incremented id"""
+        kwargs["id"] =3D self.id
+        self.id +=3D 1
+        return Node(nodeName, **kwargs)
+
+    def addRoot(self, root):
+        """Creates a root for phyloTree"""
+        assert isinstance(root, Node)
+        root.parent =3D None
+        self.root =3D root
+
+    def generateJsonableDict(self):
+        """Changes itself into a dictonary by recurssively calling the toj=
son on all its nodes. Think of it
+        as a dict in an array of dict in an array of dict and so on..."""
+        jsonTree =3D ""
+        if self.root:
+            assert isinstance(self.root, Node)
+            jsonTree =3D self.root.toJson()
+            for key, value in self.rootAttr.items():
+                # transfer temporary stored attr to root
+                jsonTree[key] =3D value
+        else:
+            raise Exception("Root is not assigned!")
+        return jsonTree
+
+
+
+class Base_Parser(object):
+    """Base parsers contain all the methods to handle phylogeny tree creat=
ion and
+    converting the data to json that all parsers should have"""
+
+    def __init__(self):
+        self.phyloTrees =3D []
+
+    def parseFile(self, filePath):
+        """Base method that all phylogeny file parser should have"""
+        raise Exception("Base method for phylogeny file parsers is not imp=
lemented")
+
+    def toJson(self, jsonDict):
+        """Convenience method to get a json string from a python json dict=
"""
+        return json.dumps(jsonDict)
+
+    def _writeJsonToFile(self, filepath, json):
+        """Writes the file out to the system"""
+        f =3D open(filepath, "w")
+        f.writelines(json)
+        f.close()


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/visualization/phyloviz/newickparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/newickparser.py
@@ -0,0 +1,185 @@
+from baseparser import Base_Parser, PhyloTree
+import re
+
+class Newick_Parser(Base_Parser):
+    """For parsing trees stored in the newick format (.nhx)
+    It is necessarily more complex because this parser is later extended b=
y Nexus for parsing newick as well.."""
+
+
+    def __init__(self):
+        super(Newick_Parser, self).__init__()
+
+
+    def parseFile(self, filePath):
+        """Parses a newick file to obtain the string inside. Returns: json=
ableDict"""
+        with open(filePath, "r") as newickFile:
+            newickString =3D newickFile.read()
+            newickString =3D newickString.replace("\n", "").replace("\r", =
"")
+            return [self.parseData(newickString)], "Success"
+
+
+    def parseData(self, newickString):
+        """To be called on a newickString directly to parse it. Returns: j=
sonableDict"""
+        return self._parseNewickToJson(newickString)
+
+
+    def _parseNewickToJson(self, newickString, treeName=3DNone, nameMap=3D=
None):
+        """parses a newick representation of a tree into a PhyloTree data =
structure,
+        which can be easily converted to json"""
+        self.phyloTree =3D PhyloTree()
+        newickString =3D self.cleanNewickString(newickString)
+        if nameMap:
+            newickString =3D self._mapName(newickString, nameMap)
+
+        self.phyloTree.root =3D self.parseNode(newickString, 0)
+        if nameMap:
+            self.phyloTree.addAttributesToRoot({"treeName": treeName})
+
+        return self.phyloTree.generateJsonableDict()
+
+
+    def cleanNewickString(self, rawNewick):
+        """removing semi colon, and illegal json characters (\,',") and wh=
ite spaces"""
+        return re.sub(r'\s|;|\"|\'|\\', '', rawNewick)
+
+
+    def _makeNodesFromString(self, string, depth):
+        """elements separated by comma could be empty"""
+
+        if string.find("(") !=3D -1:
+            raise Exception("Tree is not well form, location: " + string)
+
+        childrenString =3D string.split(",")
+        childrenNodes =3D []
+
+        for childString in childrenString:
+            if len(childString) =3D=3D 0:
+                continue
+            nodeInfo =3D childString.split(":")
+            name, length, bootstrap =3D "", None, -1
+            if len(nodeInfo) =3D=3D 2: # has length info
+                length =3D nodeInfo[1]
+                # checking for bootstap values
+                name =3D nodeInfo[0]
+                try:    # Nexus may bootstrap in names position
+                    name =3D float(name)
+                    if 0<=3D name <=3D 1:
+                        bootstrap =3D name
+                    elif 1 <=3D name <=3D 100:
+                        bootstrap =3D name / 100
+                    name =3D ""
+                except ValueError:
+                    name =3D nodeInfo[0]
+            else:
+                name =3D nodeInfo[0]      # string only contains name
+            node =3D self.phyloTree.makeNode(name, length=3Dlength, depth=
=3Ddepth, bootstrap=3D bootstrap)
+            childrenNodes +=3D [node]
+        return childrenNodes
+
+
+
+    def _mapName(self, newickString, nameMap):
+        """
+        Necessary to replace names of terms inside nexus representation
+        Also, its here because Mailaud's doesnt deal with id_strings outsi=
de of quotes(" ")
+        """
+        newString =3D ""
+        start =3D 0
+        end =3D 0
+
+        for i in xrange(len(newickString)):
+            if newickString[i] =3D=3D "(" or newickString[i] =3D=3D ",":
+                if re.match(r"[,(]", newickString[i+1:]):
+                    continue
+                else:
+                    end =3D i + 1
+                    # i now refers to the starting position of the term to=
 be replaced,
+                    # we will next find j which is the ending pos of the t=
erm
+                    for j in xrange(i+1, len(newickString)):
+                        enclosingSymbol =3D newickString[j]   # the immedi=
ate symbol after a common or left bracket which denotes the end of a term
+                        if  enclosingSymbol =3D=3D ")" or enclosingSymbol =
=3D=3D ":" or enclosingSymbol =3D=3D ",":
+                            termToReplace =3D  newickString[end:j]
+
+                            newString +=3D newickString[start : end] +  na=
meMap[termToReplace] #+ "'"  "'" +
+                            start =3D j
+                            break
+
+        newString +=3D newickString[start:]
+        return newString
+
+
+    def parseNode(self, string, depth):
+        """ Recursive method for parsing newick string, works by stripping=
 down the string into substring
+        of newick contained with brackers, which is used to call itself.
+            Eg ... ( A, B, (D, E)C, F, G ) ...
+        We will make the preceeding nodes first A, B, then the internal no=
de C, its children D, E,
+        and finally the succeeding nodes F, G"""
+
+        # Base case where there is only an empty string
+        if string =3D=3D "":
+            return
+            # Base case there its only an internal claude
+        if string.find("(") =3D=3D -1:
+            return self._makeNodesFromString(string, depth)
+
+        nodes, children =3D [], []      # nodes refer to the nodes on this=
 level, children refers to the child of the
+        start =3D 0
+        lenOfPreceedingInternalNodeString =3D 0
+        bracketStack =3D []
+
+        for j in xrange(len(string)):
+            if string[j] =3D=3D "(":    #finding the positions of all the =
open brackets
+                bracketStack.append(j)
+                continue
+            if string[j] =3D=3D ")":    #finding the positions of all the =
closed brackets to extract claude
+                i =3D bracketStack.pop()
+
+                if len(bracketStack) =3D=3D 0:  # is child of current node
+
+                    InternalNode =3D None
+
+                    #First flat call to make nodes of the same depth but f=
rom the preceeding string.
+                    startSubstring =3D string[start + lenOfPreceedingInter=
nalNodeString: i]
+                    preceedingNodes =3D  self._makeNodesFromString(startSu=
bstring, depth)
+                    nodes +=3D preceedingNodes
+
+                    # Then We will try to see if the substring has any int=
ernal nodes first, make it then make nodes preceeding it and succeeding it.
+                    if j + 1 < len(string):
+                        stringRightOfBracket =3D string[j+1:]      # Eg. '=
(b:0.4,a:0.3)c:0.3, stringRightOfBracket =3D c:0.3
+                        match =3D re.search(r"[\)\,\(]", stringRightOfBrac=
ket)
+                        if match:
+                            indexOfNextSymbol =3D match.start()
+                            stringRepOfInternalNode =3D stringRightOfBrack=
et[:indexOfNextSymbol]
+                            internalNodes =3D self._makeNodesFromString( s=
tringRepOfInternalNode, depth)
+                            if len(internalNodes) > 0:
+                                InternalNode =3D internalNodes[0]
+                            lenOfPreceedingInternalNodeString =3D len(stri=
ngRepOfInternalNode)
+                        else:   # sometimes the node can be the last eleme=
nt of a string
+                            InternalNode =3D self._makeNodesFromString(str=
ing[j+1:], depth)[0]
+                            lenOfPreceedingInternalNodeString =3D len(stri=
ng) - j
+                    if InternalNode =3D=3D None:       #creating a generic=
 node if it is unnamed
+                        InternalNode =3D self.phyloTree.makeNode( "", dept=
h=3Ddepth, isInternal=3DTrue ) #"internal-" + str(depth)
+                        lenOfPreceedingInternalNodeString =3D 0
+
+                    # recussive call to make the internal claude
+                    childSubString =3D string[ i + 1 : j ]
+                    InternalNode.addChildNode(self.parseNode(childSubStrin=
g, depth + 1))
+
+                    nodes.append(InternalNode)  # we append the internal n=
ode later to preserve order
+
+                    start =3D j + 1
+                continue
+
+        if depth =3D=3D 0:    # if its the root node, we do nothing about =
it and return
+            return nodes[0]
+
+        # Adding last most set of children
+        endString =3D string[start:]
+        if string[start-1] =3D=3D ")":  # if the symbol belongs to an inte=
rnal node which is created previously, then we remove it from the string le=
ft to parse
+            match =3D re.search(r"[\)\,\(]", endString)
+            if match:
+                endOfNodeName =3D start + match.start() + 1
+                endString =3D string[endOfNodeName:]
+                nodes +=3D self._makeNodesFromString(endString, depth)
+
+        return nodes


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/visualization/phyloviz/nexusparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/nexusparser.py
@@ -0,0 +1,107 @@
+from newickparser import Newick_Parser
+import re
+
+MAX_READLINES =3D 200000
+
+
+class Nexus_Parser(Newick_Parser):
+
+    def __init__(self):
+        super(Nexus_Parser, self).__init__()
+
+    def parseFile(self, filePath):
+        """passes a file and extracts its Nexus content."""
+        return self.parseNexus(filePath)
+
+
+    def parseNexus(self, filename):
+        """ Nexus data is stored in blocks between a line starting with be=
gin and another line starting with end;
+        Commends inside square brackets are to be ignored,
+        For more information: http://wiki.christophchamp.com/index.php/NEX=
US_file_format
+        Nexus can store multiple trees
+        """
+
+        with open( filename, "rt") as nex_file:
+            nexlines =3D nex_file.readlines()
+
+        rowCount =3D 0
+        inTreeBlock =3D False         # sentinel to check if we are in a t=
ree block
+        intranslateBlock =3D False    # sentinel to check if we are in the=
 translate region of the tree. Stores synonyms of the labellings
+        self.inCommentBlock =3D False
+        self.nameMapping =3D None       # stores mapping representation us=
ed in nexus format
+        treeNames =3D []
+
+        for line in nexlines:
+            line =3D line.replace(";\n", "")
+            lline =3D line.lower()
+
+            if rowCount > MAX_READLINES or (not nex_file) :
+                break
+            rowCount +=3D1
+            # We are only interested in the tree block.
+            if "begin" in lline and "tree" in lline and not inTreeBlock:
+                inTreeBlock =3D True
+                continue
+            if inTreeBlock and "end" in lline[:3]:
+                inTreeBlock, currPhyloTree =3D False, None
+                continue
+
+            if inTreeBlock:
+
+                if "title" in lline:        # Adding title to the tree
+                    titleLoc =3D lline.find("title")
+                    title =3D line[titleLoc + 5:].replace(" ", "")
+
+                    continue
+
+                if "translate" in lline:
+                    intranslateBlock =3D True
+                    self.nameMapping =3D {}
+                    continue
+
+                if intranslateBlock:
+                    mappingLine =3D self.splitLinebyWhitespaces(line)
+                    key, value =3D mappingLine[1], mappingLine[2].replace(=
",", "").replace("'","")    #replacing illegal json characters
+                    self.nameMapping[key] =3D value
+
+                # Extracting newick Trees
+                if "tree" in lline:
+                    intranslateBlock =3D False
+
+                    treeLineCols =3D self.splitLinebyWhitespaces(line)
+                    treeName, newick =3D treeLineCols[2], treeLineCols[-1]
+
+                    if newick =3D=3D "":    # Empty lines can be found in =
tree blocks
+                        continue
+
+                    currPhyloTree =3D self._parseNewickToJson(newick, tree=
Name, nameMap=3Dself.nameMapping)
+
+                    self.phyloTrees.append(currPhyloTree)
+                    treeIndex =3D len(self.phyloTrees) - 1
+                    treeNames.append( (treeName, treeIndex) )    # appendi=
ng name of tree, and its index
+                    continue
+
+        return self.phyloTrees, treeNames
+
+
+    def splitLinebyWhitespaces(self, line):
+        """replace tabs and write spaces to a single write space, so we ca=
n properly split it."""
+        return re.split(r"\s+", line)
+
+
+    def checkComments(self, line):
+        """Check to see if the line/lines is a comment."""
+        if not self.inCommentBlock:
+            if "[" in line:
+                if "]" not in line:
+                    self.inCommentBlock =3D True
+                else:
+                    return "Nextline"   # need to move on to the nextline =
after getting out of comment
+        else :
+            if "]" in line:
+                if line.rfind("[") > line.rfind("]"):
+                    pass                # a comment block is closed but an=
other is open.
+                else:
+                    self.inCommentBlock =3D False
+                    return "Nextline"   # need to move on to the nextline =
after getting out of comment
+        return ""
\ No newline at end of file


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py
@@ -0,0 +1,35 @@
+from newickparser import Newick_Parser
+from nexusparser import Nexus_Parser
+from phyloxmlparser import Phyloxml_Parser
+
+class Phyloviz_DataProvider(object):
+
+    def __init__(self):
+        pass
+
+    def parseFile(self, filepath, fileExt):
+        """returns [trees], meta
+            Trees are actually an array of JsonDicts. It's usually one tre=
e, except in the case of Nexus
+        """
+        jsonDicts, meta =3D [], {}
+        try:
+            if fileExt =3D=3D "nhx": # parses newick files
+                newickParser =3D Newick_Parser()
+                jsonDicts, parseMsg =3D newickParser.parseFile(filepath)
+            elif fileExt =3D=3D "phyloxml": # parses phyloXML files
+                phyloxmlParser =3D Phyloxml_Parser()
+                jsonDicts, parseMsg =3D phyloxmlParser.parseFile(filepath)
+            elif fileExt =3D=3D "nex": # parses nexus files
+                nexusParser =3D Nexus_Parser()
+                jsonDicts, parseMsg =3D nexusParser.parseFile(filepath)
+                meta["trees"] =3D parseMsg
+            else:
+                raise Exception("File type is not supported")
+
+            meta["msg"] =3D parseMsg
+
+        except Exception:
+            jsonDicts, meta["msg"] =3D [], "Parse failed"
+
+        return jsonDicts, meta
+


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/visualization/phyloviz/phyloxmlparser.py
--- /dev/null
+++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py
@@ -0,0 +1,145 @@
+from baseparser import Base_Parser, PhyloTree, Node
+from lxml import etree
+
+class Phyloxml_Parser(Base_Parser):
+    """Parses a phyloxml file into a json file that will be passed to Phyl=
oViz for display"""
+
+    def __init__(self):
+        super(Phyloxml_Parser, self).__init__()
+        self.phyloTree =3D PhyloTree()
+        self.tagsOfInterest =3D {
+            "clade": "",
+            "name" : "name",
+            "branch_length" : "length",
+            "confidence"    : "bootstrap",
+            "events"        : "events"
+        }
+
+    def parseFile(self, filePath):
+        """passes a file and extracts its Phylogeny Tree content."""
+        phyloXmlFile =3D open(filePath, "r")
+
+        xmlTree =3D etree.parse(phyloXmlFile)
+        xmlRoot =3D xmlTree.getroot()[0]
+        self.nameSpaceIndex =3D xmlRoot.tag.rfind("}") + 1 # used later by=
 the clean tag method to remove the name space in every element.tag
+
+        phyloRoot =3D None
+        for child in xmlRoot:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "clade":
+                phyloRoot =3D child
+            elif childTag =3D=3D "name":
+                self.phyloTree.title =3D child.text
+
+        self.phyloTree.root =3D self.parseNode(phyloRoot, 0)
+        jsonDict =3D self.phyloTree.generateJsonableDict()
+        return [jsonDict], "Success"
+
+
+    def parseNode(self, node, depth):
+        """Parses any node within a phyloxml tree and looks out for claude=
, which signals the creation of
+        nodes - internal OR leaf"""
+        assert isinstance(node, etree._Element)
+
+        tag =3D self.cleanTag(node.tag)
+        if not tag =3D=3D "clade":
+            return None
+        hasInnerClade =3D False
+
+        # peeking once for parent and once for child to check if the node =
is internal
+        for child in node:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "clade":
+                hasInnerClade =3D True
+                break
+
+        if hasInnerClade:       # this node is an internal node
+            currentNode =3D self._makeInternalNode(node, depth=3D depth)
+            for child in node:
+                child =3D self.parseNode(child, depth + 1)
+                if isinstance(child, Node):
+                    currentNode.addChildNode(child)
+
+        else:                   # this node is a leaf node
+            currentNode =3D self._makeLeafNode(node, depth=3Ddepth+1)
+
+        return currentNode
+
+
+    def _makeLeafNode(self, leafNode, depth =3D 0 ):
+        """Makes leaf nodes by calling Phylotree methods"""
+        node =3D {}
+        for child in leafNode:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag in self.tagsOfInterest:
+                key =3D self.tagsOfInterest[childTag]    # need to map phy=
loxml terms to ours
+                node[key] =3D child.text
+
+        node["depth"] =3D depth
+        return self.phyloTree.makeNode(self._getNodeName(leafNode), **node)
+
+    def _getNodeName(self, node, depth=3D-1):
+        """Gets the name of a claude. It handles the case where a taxonomy=
 node is involved"""
+
+        def getTagFromTaxonomyNode(node):
+            """Returns the name of a taxonomy node. A taxonomy node have t=
o be treated differently as the name
+            is embedded one level deeper"""
+            phyloxmlTaxoNames =3D {
+                "common_name" : "",
+                "scientific_name" : "",
+                "code"  : ""
+            }
+            for child in node:
+                childTag =3D self.cleanTag(child.tag)
+                if childTag in phyloxmlTaxoNames:
+                    return child.text
+            return ""
+
+        nodeName =3D ""
+        for child in node:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "name" :
+                nodeName =3D child.text
+                break
+            elif childTag =3D=3D "taxonomy":
+                nodeName =3D getTagFromTaxonomyNode(child)
+                break
+
+        return nodeName
+
+
+    def _makeInternalNode(self, internalNode, depth=3D0):
+        """ Makes an internal node from an element object that is gurantee=
d to be a parent node.
+        Gets the value of interests like events and appends it to a custom=
 node object that will be passed to PhyloTree to make nodes
+        """
+        node =3D {}
+        for child in internalNode:
+            childTag =3D self.cleanTag(child.tag)
+            if childTag =3D=3D "clade":
+                continue
+            elif childTag in self.tagsOfInterest:
+                if childTag =3D=3D "events":    # events is nested 1 more =
level deeper than others
+                    key, text =3D "events", self.cleanTag(child[0].tag)
+                else:
+                    key =3D self.tagsOfInterest[childTag]
+                    text =3D child.text
+                node[key] =3D text
+
+
+        return self.phyloTree.makeNode(self._getNodeName(internalNode, dep=
th), **node)
+
+
+    def cleanTag(self, tagString):
+        return tagString[self.nameSpaceIndex:]
+
+
+if __name__=3D=3D"__main__":
+
+    # Files tested against
+    parser =3D Phyloxml_Parser()
+    filepath =3D "../data/" +"apaf.xml"
+    #    filepath =3D "../data/" +"12_multiple_supports.xml"
+
+    #    filepath =3D "../data/" +"bcl_2.xml"
+    #    filepath =3D "../data/" +"reducedXml.xml"
+    parser.parseFile(filepath)


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/web/controllers/phyloviz.py
--- /dev/null
+++ b/lib/galaxy/web/controllers/phyloviz.py
@@ -0,0 +1,97 @@
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+from galaxy.util.json import to_json_string, from_json_string
+from galaxy.web.base.controller import *
+from galaxy.visualization.phyloviz.phyloviz_dataprovider import Phyloviz_D=
ataProvider
+
+
+class PhyloVizController( BaseUIController, UsesVisualizationMixin, UsesHi=
storyDatasetAssociationMixin, SharableMixin ):
+    """
+    Controller for phyloViz browser interface.
+    """
+    def __init__(self, app ):
+        BaseUIController.__init__( self, app )
+
+    @web.expose
+    @web.require_login()
+    def index( self, trans, dataset_id =3D None, **kwargs ):
+        """
+        The index method is called using phyloviz/ with a dataset id passe=
d in.
+        The relevant data set is then retrieved via get_json_from_datasetI=
d which interfaces with the parser
+        The json representation of the phylogenetic tree along with the co=
nfig is then written in the .mako template and passed back to the user
+        """
+        json, config =3D self.get_json_from_datasetId(trans, dataset_id)
+        config["saved_visualization"] =3D False
+        return trans.fill_template( "visualization/phyloviz.mako", data =
=3D json, config=3Dconfig)
+
+
+    @web.expose
+    def visualization(self, trans, id):
+        """
+        Called using a viz_id (id) to retrieved stored visualization data =
(in json format) and all the viz_config
+        """
+        viz =3D self.get_visualization(trans, id)
+        config =3D self.get_visualization_config(trans, viz)
+        config["saved_visualization"] =3D True
+        data =3D config["root"]
+
+        return trans.fill_template( "visualization/phyloviz.mako", data =
=3D data, config=3Dconfig)
+
+
+    @web.expose
+    @web.json
+    def load_visualization_json(self, trans, viz_id):
+        """
+        Though not used in current implementation, this provides user with=
 a convenient method to retrieve the viz_data & viz_config via json.
+        """
+        viz =3D self.get_visualization(trans, viz_id)
+        viz_config =3D self.get_visualization_config(trans, viz)
+        viz_config["saved_visualization"] =3D True
+        return {
+            "data" : viz_config["root"],
+            "config" : viz_config
+        }
+
+
+    @web.expose
+    @web.json
+    def getJsonData(self, trans, dataset_id, treeIndex=3D0):
+        """
+        Method to retrieve data asynchronously via json format. Retriving =
from here rather than
+        making a direct datasets/ call allows for some processing and even=
t capturing
+        """
+        treeIndex =3D int(treeIndex)
+        json, config =3D self.get_json_from_datasetId(trans, dataset_id, t=
reeIndex)
+        packedJson =3D {
+            "data" : json,
+            "config" : config
+        }
+
+        return packedJson
+
+
+    def get_json_from_datasetId(self, trans, dataset_id, treeIndex=3D0):
+        """
+        For interfacing phyloviz controllers with phyloviz visualization d=
ata provider (parsers)
+        """
+        dataset =3D self.get_dataset(trans, dataset_id)
+        fileExt, filepath  =3D dataset.ext, dataset.file_name      # .name=
 stores the name of the dataset from the orginal upload
+        json, config =3D "", {}         #        config contains propertie=
s of the tree and file
+
+        if fileExt =3D=3D "json":
+            something, json =3D self.get_data(dataset)
+        else:
+            try:
+                pd =3D Phyloviz_DataProvider()
+                json, config =3D pd.parseFile(filepath, fileExt)
+                json =3D json[treeIndex]
+            except Exception:
+                pass
+
+        config["title"] =3D dataset.display_name()
+        config["ext"] =3D fileExt
+        config["dataset_id"] =3D dataset_id
+        config["treeIndex"] =3D treeIndex
+
+        return json, config


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -16,6 +16,10 @@
             action =3D "paramamonster"
         elif item.type =3D=3D "circster":
             action =3D "circster"
+        elif item.type =3D=3D "phyloviz":
+            # Support phyloviz
+            controller =3D "phyloviz"
+            action =3D "visualization"
         return dict( controller=3Dcontroller, action=3Daction, id=3Ditem.i=
d )
=20
     # Grid definition


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 static/scripts/viz/phyloviz.js
--- /dev/null
+++ b/static/scripts/viz/phyloviz.js
@@ -0,0 +1,955 @@
+var UserMenuBase =3D Backbone.View.extend({
+    /**
+     * Base class of any menus that takes in user interaction. Contains ch=
ecking methods.
+     */
+
+    className: 'UserMenuBase',
+
+    isAcceptableValue : function ($inputKey, min, max) {
+        /**
+         * Check if an input value is a number and falls within max min.
+         */
+        var self =3D this,
+            value =3D $inputKey.val(),
+            fieldName =3D $inputKey.attr("displayLabel") || $inputKey.attr=
("id").replace("phyloViz", "");
+
+        function isNumeric(n) {
+            return !isNaN(parseFloat(n)) && isFinite(n);
+        }
+
+        if (!isNumeric(value)){
+            alert(fieldName + " is not a number!");
+            return false;
+        }
+
+        if ( value > max){
+            alert(fieldName + " is too large.");
+            return false;
+        } else if ( value < min) {
+            alert(fieldName + " is too small.");
+            return false;
+        }
+        return true;
+    },
+
+    hasIllegalJsonCharacters : function($inputKey) {
+        /**
+         * Check if any user string inputs has illegal characters that jso=
n cannot accept
+         */
+        if ($inputKey.val().search(/"|'|\\/) !=3D=3D -1){
+            alert("Named fields cannot contain these illegal characters: d=
ouble quote(\"), single guote(\'), or back slash(\\). ");
+            return true;
+        }
+        return false;
+    }
+});
+
+
+function PhyloTreeLayout() {
+    /**
+     * -- Custom Layout call for phyloViz to suit the needs of a phylogene=
tic tree.
+     * -- Specifically: 1) Nodes have a display display of (=3D evo dist X=
 depth separation) from their parent
+     *                  2) Nodes must appear in other after they have expa=
nd and contracted
+     */
+
+    var self =3D this,
+        hierarchy =3D d3.layout.hierarchy().sort(null).value(null),
+        height =3D 360, // ! represents both the layout angle and the heig=
ht of the layout, in px
+        layoutMode =3D "Linear",
+        leafHeight =3D 18, // height of each individual leaf node
+        depthSeparation =3D 200, // separation between nodes of different =
depth, in px
+        leafIndex =3D 0, // change to recurssive call
+        defaultDist =3D 0.5, // tree defaults to 0.5 dist if no dist is sp=
ecified
+        maxTextWidth =3D 50; // maximum length of the text labels
+
+
+    self.leafHeight =3D function(inputLeafHeight){
+        if (typeof inputLeafHeight =3D=3D=3D "undefined"){ return leafHeig=
ht; }
+        else { leafHeight =3D inputLeafHeight; return self;}
+    };
+
+    self.layoutMode =3D function(mode){
+        if (typeof mode =3D=3D=3D "undefined"){ return layoutMode; }
+        else { layoutMode =3D mode; return self;}
+    };
+
+    self.layoutAngle =3D function(angle) {    // changes the layout angle =
of the display, which is really changing the height
+        if (typeof angle =3D=3D=3D "undefined"){ return height; }
+        if (isNaN(angle) || angle < 0 || angle > 360) { return self; } // =
to use default if the user puts in strange values
+        else { height =3D angle; return self;}
+    };
+
+    self.separation =3D function(dist){   // changes the dist between the =
nodes of different depth
+        if (typeof dist =3D=3D=3D "undefined"){ return depthSeparation; }
+        else { depthSeparation =3D dist; return self;}
+    };
+
+    self.links =3D function (nodes) {     // uses d3 native method to gene=
rate links. Done.
+        return d3.layout.tree().links(nodes);
+    };
+
+    // -- Custom method for laying out phylogeny tree in a linear fashion
+    self.nodes =3D function (d, i) {
+        var _nodes =3D hierarchy.call(self, d, i),         // self is to f=
ind the depth of all the nodes, assumes root is passed in
+            nodes =3D [],
+            maxDepth =3D 0,
+            numLeaves =3D 0;
+
+        // changing from hierarchy's custom format for data to usable form=
at
+        _nodes.forEach(function (_node){
+            var node =3D _node.data;
+            node.depth =3D _node.depth;
+            maxDepth =3D node.depth > maxDepth ? node.depth : maxDepth;  /=
/finding max depth of tree
+            nodes.push(node);
+        });
+        // counting the number of leaf nodes and assigning max depth to no=
des that do not have children to flush all the leave nodes
+        nodes.forEach(function(node){
+            if ( !node.children )  { //&& !node._children
+                numLeaves +=3D 1;
+                node.depth =3D maxDepth; // if a leaf has no child it woul=
d be assigned max depth
+            }
+        });
+
+        leafHeight =3D layoutMode =3D=3D=3D "Circular" ? height / numLeave=
s : leafHeight;
+        leafIndex =3D 0;
+        layout(nodes[0], maxDepth, leafHeight, null);
+
+        return nodes;
+    };
+
+
+    function layout (node, maxDepth, vertSeparation, parent) {
+        /**
+         * -- Function with side effect of adding x0, y0 to all child; tak=
e in the root as starting point
+         *  assuming that the leave nodes would be sorted in presented ord=
er
+         *          horizontal(y0) is calculated according to (=3D evo dis=
t X depth separation) from their parent
+         *          vertical (x0) - if leave node: find its order in all o=
f the  leave node =3D=3D=3D node.id, then multiply by verticalSeparation
+         *                  - if parent node: is place in the mid point al=
l of its children nodes
+         * -- The layout will first calculate the y0 field going towards t=
he leaves, and x0 when returning
+         */
+        var children =3D node.children,
+            sumChildVertSeparation =3D 0;
+
+        // calculation of node's dist from parents, going down.
+        var dist =3D node.dist || defaultDist;
+        dist =3D dist > 1 ? 1 : dist;     // We constrain all dist to be l=
ess than one
+        node.dist =3D dist;
+        if (parent !=3D=3D null){
+            node.y0 =3D parent.y0 + dist * depthSeparation;
+        } else {    //root node
+            node.y0 =3D maxTextWidth;
+        }
+
+
+        // if a node have no children, we will treat it as a leaf and star=
t laying it out first
+        if (!children) {
+            node.x0 =3D leafIndex++ * vertSeparation;
+        } else {
+            // if it has children, we will visit all its children and calc=
ulate its position from its children
+            children.forEach( function (child) {
+                child.parent =3D node;
+                sumChildVertSeparation +=3D layout(child, maxDepth, vertSe=
paration, node);
+            });
+            node.x0 =3D sumChildVertSeparation / children.length;
+        }
+
+        // adding properties to the newly created node
+        node.x =3D node.x0;
+        node.y =3D node.y0;
+        return node.x0;
+    }
+    return self;
+}
+
+
+/**
+ * -- PhyloTree Model --
+ */
+var PhyloTree =3D Visualization.extend({
+    defaults : {
+        layout: "Linear",
+        separation : 250,    // px dist between nodes of different depth t=
o represent 1 evolutionary until
+        leafHeight: 18,
+        type : "phyloviz",   // visualization type
+        title : "Title",
+        scaleFactor: 1,
+        translate: [0,0],
+        fontSize: 12,        //fontSize of node label
+        selectedNode : null,
+        nodeAttrChangedTime : 0
+    },
+
+    root : {}, // Root has to be its own independent object because it is =
not part of the viz_config
+
+    toggle : function (d) {
+        /**
+         * Mechanism to expand or contract a single node. Expanded nodes h=
ave a children list, while for
+         * contracted nodes the list is stored in _children. Nodes with th=
eir children data stored in _children will not have their
+         * children rendered.
+         */
+        if(typeof d =3D=3D=3D "undefined") {return ;}
+        if (d.children ) {
+            d._children =3D d.children;
+            d.children =3D null;
+        } else {
+            d.children =3D d._children;
+            d._children =3D null;
+        }
+    },
+
+    toggleAll : function(d) {
+        /**
+         *  Contracts the phylotree to a single node by repeatedly calling=
 itself to place all the list
+         *  of children under _children.
+         */
+        if (d.children && d.children.length !=3D=3D 0) {
+            d.children.forEach(this.toggleAll);
+            toggle(d);
+        }
+    },
+
+    getData : function (){
+        /**
+         *  Return the data of the tree. Used for preserving state.
+         */
+        return this.root;
+    },
+
+    save: function() {
+        /**
+         * Overriding the default save mechanism to do some clean of circu=
lar reference of the
+         * phyloTree and to include phyloTree in the saved json
+         */
+        var root =3D this.root;
+        cleanTree(root);
+        this.set("root", root);
+
+        function cleanTree(node){
+            // we need to remove parent to delete circular reference
+            delete node.parent;
+
+            // removing unnecessary attributes
+            if (node._selected){ delete node._selected;}
+
+            node.children ? node.children.forEach(cleanTree) : 0;
+            node._children ? node._children.forEach(cleanTree) : 0;
+        }
+
+        var config  =3D jQuery.extend(true, {}, this.attributes);
+        config["selectedNode"] =3D null;
+
+        show_message("Saving to Galaxy", "progress");
+
+        return $.ajax({
+            url: this.url(),
+            type: "POST",
+            dataType: "json",
+            data: {
+                vis_json: JSON.stringify(config)
+            },
+            success: function(res){
+                var viz_id =3D res.url.split("id=3D")[1].split("&")[0],
+                    viz_url =3D "/phyloviz/visualization?id=3D" + viz_id;
+                window.history.pushState({}, "", viz_url + window.location=
.hash);
+                hide_modal();
+            }
+        });
+    }
+});
+
+
+
+/**
+ * -- Views --
+ */
+var PhylovizLayoutBase =3D  Backbone.View.extend({
+    /**
+     *  Stores the default variable for setting up the visualization
+     */
+    defaults : {
+        nodeRadius : 4.5 // radius of each node in the diagram
+    },
+
+
+    stdInit : function (options) {
+        /**
+         *  Common initialization in layouts
+         */
+
+        var self =3D this;
+        self.model.on("change:separation change:leafHeight change:fontSize=
 change:nodeAttrChangedTime", self.updateAndRender, self);
+
+        self.vis =3D options.vis;
+        self.i =3D 0;
+        self.maxDepth =3D -1; // stores the max depth of the tree
+
+        self.width =3D options.width;
+        self.height =3D options.height;
+    },
+
+
+    updateAndRender : function(source) {
+        /**
+         *  Updates the visualization whenever there are changes in the ex=
pansion and contraction of nodes
+         *  AND possibly when the tree is edited.
+         */
+        var vis =3D d3.select(".vis"),
+            self =3D this;
+        source =3D source || self.model.root;
+
+        self.renderNodes(source);
+        self.renderLinks(source);
+        self.addTooltips();
+    },
+
+
+    renderLinks : function(source) {
+        /**
+         * Renders the links for the visualization.
+         */
+        var self =3D this;
+        var diagonal =3D self.diagonal;
+        var duration =3D self.duration;
+        var layoutMode =3D self.layoutMode;
+        var link =3D self.vis.selectAll("g.completeLink")
+            .data(self.tree.links(self.nodes), function(d) { return d.targ=
et.id; });
+
+        var calcalateLinePos =3D function(d) {
+            d.pos0 =3D d.source.y0 + " " + d.source.x0;   // position of t=
he source node <=3D> starting location of the line drawn
+            d.pos1 =3D d.source.y0 + " " + d.target.x0;  // position where=
 the line makes a right angle bend
+            d.pos2 =3D d.target.y0 + " " + d.target.x0;     // point where=
 the horizontal line becomes a dotted line
+        };
+
+        var linkEnter =3D link.enter().insert("svg:g","g.node")
+            .attr("class", "completeLink");
+
+
+        linkEnter.append("svg:path")
+            .attr("class", "link")
+            .attr("d", function(d) {
+                calcalateLinePos(d);
+                return "M " + d.pos0  + " L " + d.pos1;
+            });
+
+        var linkUpdate =3D link.transition().duration(500);
+
+        linkUpdate.select("path.link")
+            .attr("d", function(d) {
+                calcalateLinePos(d);
+                return "M " + d.pos0 + " L " + d.pos1 + " L " + d.pos2;
+            });
+
+        var linkExit =3D link.exit().remove();
+
+    },
+
+    // User Interaction methods below
+
+    selectNode : function(node){
+        /**
+         *  Displays the information for editting
+         */
+        var self =3D this;
+        d3.selectAll("g.node")
+            .classed("selectedHighlight", function(d){
+                if (node.id =3D=3D=3D d.id){
+                    if(node._selected) { // for de=3Dselecting node.
+                        delete node._selected;
+                        return false;
+                    } else {
+                        node._selected =3D true;
+                        return true;
+                    }
+                }
+                return false;
+            });
+
+        self.model.set("selectedNode", node);
+        $("#phyloVizSelectedNodeName").val(node.name);
+        $("#phyloVizSelectedNodeDist").val(node.dist);
+        $("#phyloVizSelectedNodeAnnotation").val(node.annotation || "");
+    },
+
+    addTooltips : function (){
+        /**
+         *  Creates bootstrap tooltip for the visualization. Has to be cal=
led repeatedly due to newly generated
+         *  enterNodes
+         */
+        $(".bs-tooltip").remove();      //clean up tooltip, just in case i=
ts listeners are removed by d3
+        $(".node")
+            .attr("data-original-title", function(){
+                var d =3D this.__data__,
+                    annotation =3D d.annotation || "None" ;
+                return d ? (d.name ? d.name + "<br/>" : "") + "Dist: " + d=
.dist + " <br/>Annotation: " + annotation: "";
+            })
+            .tooltip({'placement':'top', 'trigger' : 'hover'});
+
+    }
+});
+
+
+
+
+var PhylovizLinearView =3D  PhylovizLayoutBase.extend({
+    /**
+     * Linea layout class of Phyloviz, is responsible for rendering the no=
des
+     * calls PhyloTreeLayout to determine the positions of the nodes
+     */
+    initialize : function(options){
+        // Default values of linear layout
+        var self =3D this;
+        self.margins =3D options.margins;
+        self.layoutMode =3D "Linear";
+
+        self.stdInit(options);
+
+        self.layout();
+        self.updateAndRender(self.model.root);
+    },
+
+    layout : function() {
+        /**
+         * Creates the basic layout of a linear tree by precalculating fix=
ed values.
+         * One of calculations are also made here
+         */
+
+        var self =3D this;
+
+        self.tree =3D new PhyloTreeLayout().layoutMode("Linear");
+        self.diagonal =3D d3.svg.diagonal()
+            .projection(function(d) { return [d.y, d.x ]; });
+    },
+
+    renderNodes : function (source) {
+        /**
+         * Renders the nodes base on Linear layout.
+         */
+        var self =3D this,
+            fontSize =3D self.model.get("fontSize") + "px";
+
+        // assigning properties from models
+        self.tree.separation(self.model.get("separation")).leafHeight(self=
.model.get("leafHeight"));
+
+        var duration =3D 500,
+            nodes =3D self.tree.separation(self.model.get("separation")).n=
odes(self.model.root);
+
+        var node =3D self.vis.selectAll("g.node")
+            .data(nodes, function(d) { return d.name + d.id || (d.id =3D +=
+self.i); });
+
+        // These variables has to be passed into update links which are in=
 the base methods
+        self.nodes =3D nodes;
+        self.duration =3D duration;
+
+        // ------- D3 ENTRY --------
+        // Enter any new nodes at the parent's previous position.
+        var nodeEnter =3D node.enter().append("svg:g")
+            .attr("class", "node")
+            .on("dblclick", function(){ d3.event.stopPropagation();    })
+            .on("click", function(d) {
+                if (d3.event.altKey) {
+                    self.selectNode(d);        // display info if alt is p=
ressed
+                } else {
+                    if(d.children && d.children.length =3D=3D=3D 0){ retur=
n;}  // there is no need to toggle leaves
+                    self.model.toggle(d);   // contract/expand nodes at da=
ta level
+                    self.updateAndRender(d);   // re-render the tree
+                }
+            });
+
+        nodeEnter.attr("transform", function(d) { return "translate(" + so=
urce.y0 + "," + source.x0 + ")"; });
+
+        nodeEnter.append("svg:circle")
+            .attr("r", 1e-6)
+            .style("fill", function(d) { return d._children ? "lightsteelb=
lue" : "#fff"; });
+
+        nodeEnter.append("svg:text")
+            .attr("class", "nodeLabel")
+            .attr("x", function(d) { return d.children || d._children ? -1=
0 : 10; })
+            .attr("dy", ".35em")
+            .attr("text-anchor", function(d) { return d.children || d._chi=
ldren ? "end" : "start"; })
+            .style("fill-opacity", 1e-6);
+
+        // ------- D3 TRANSITION --------
+        // Transition nodes to their new position.
+        var nodeUpdate =3D node.transition()
+            .duration(duration);
+
+        nodeUpdate.attr("transform", function(d) {
+            return "translate(" + d.y + "," + d.x + ")"; });
+
+        nodeUpdate.select("circle")
+            .attr("r", self.defaults.nodeRadius)
+            .style("fill", function(d) { return d._children ? "lightsteelb=
lue" : "#fff"; });
+
+        nodeUpdate.select("text")
+            .style("fill-opacity", 1)
+            .style("font-size", fontSize)
+            .text(function(d) { return d.name; });
+
+        // ------- D3 EXIT --------
+        // Transition exiting nodes to the parent's new position.
+        var nodeExit =3Dnode.exit().transition()
+            .duration(duration)
+            .remove();
+
+        nodeExit.select("circle")
+            .attr("r", 1e-6);
+
+        nodeExit.select("text")
+            .style("fill-opacity", 1e-6);
+
+        // Stash the old positions for transition.
+        nodes.forEach(function(d) {
+            d.x0 =3D d.x; // we need the x0, y0 for parents with children
+            d.y0 =3D d.y;
+        });
+    }
+
+});
+
+var PhylovizView =3D Backbone.View.extend({
+
+    className: 'phyloviz',
+
+    initialize: function(options) {
+        var self =3D this;
+        // -- Default values of the vis
+        self.MIN_SCALE =3D 0.05; //for zooming
+        self.MAX_SCALE =3D 5;
+        self.MAX_DISPLACEMENT =3D 500;
+        self.margins =3D [10, 60, 10, 80];
+
+        self.width =3D $("#PhyloViz").width();
+        self.height =3D $("#PhyloViz").height();
+        self.radius =3D self.width;
+        self.data =3D options.data;
+
+        // -- Events Phyloviz view responses to
+        $(window).resize(function(){
+            self.width =3D $("#PhyloViz").width();
+            self.height =3D $("#PhyloViz").height();
+            self.render();
+        });
+
+        // -- Create phyloTree model
+        self.phyloTree =3D new PhyloTree(options.config);
+        self.phyloTree.root =3D self.data;
+
+        // -- Set up UI functions of main view
+        self.zoomFunc =3D d3.behavior.zoom().scaleExtent([self.MIN_SCALE, =
self.MAX_SCALE]);
+        self.zoomFunc.translate(self.phyloTree.get("translate"));
+        self.zoomFunc.scale(self.phyloTree.get("scaleFactor"));
+
+        // -- set up header buttons, search and settings menu
+        self.navMenu =3D new HeaderButtons(self);
+        self.settingsMenu =3D new SettingsMenu({phyloTree : self.phyloTree=
});
+        self.nodeSelectionView =3D new NodeSelectionView({phyloTree : self=
.phyloTree});
+        self.search =3D new PhyloVizSearch();
+
+
+        setTimeout(function(){      // using settimeout to call the zoomAn=
dPan function according to the stored attributes in viz_config
+            self.zoomAndPan();
+        }, 1000);
+    },
+
+    render: function(){
+        // -- Creating helper function for vis. --
+        var self =3D this;
+        $("#PhyloViz").empty();
+
+        // -- Layout viz. --
+        self.mainSVG =3D d3.select("#PhyloViz").append("svg:svg")
+            .attr("width", self.width)
+            .attr("height", self.height)
+            .attr("pointer-events", "all")
+            .call(self.zoomFunc.on("zoom", function(){
+            self.zoomAndPan();
+        }));
+
+        self.boundingRect =3D self.mainSVG.append("svg:rect")
+            .attr("class", "boundingRect")
+            .attr("width", self.width)
+            .attr("height", self.height)
+            .attr("stroke", "black")
+            .attr("fill", "white");
+
+        self.vis =3D self.mainSVG
+            .append("svg:g")
+            .attr("class", "vis");
+
+        self.layoutOptions =3D {
+            model : self.phyloTree,
+            width : self.width,
+            height : self.height,
+            vis: self.vis,
+            margins: self.margins
+        };
+
+        // -- Creating Title
+        $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("t=
itle") + ":");
+
+        // -- Create Linear view instance --
+        var linearView =3D new PhylovizLinearView(self.layoutOptions)
+    },
+
+    zoomAndPan : function(event){
+        /**
+         * Function to zoom and pan the svg element which the entire tree =
is contained within
+         * Uses d3.zoom events, and extend them to allow manual updates an=
d keeping states in model
+         */
+        if (typeof event !=3D=3D "undefined") {
+            var zoomParams =3D event.zoom,
+                translateParams =3D event.translate;
+        }
+
+        var self =3D this,
+            scaleFactor =3D self.zoomFunc.scale(),
+            translationCoor =3D self.zoomFunc.translate(),
+            zoomStatement =3D "",
+            translateStatement =3D "";
+
+        // Do manual scaling.
+        switch (zoomParams) {
+            case "reset":
+                scaleFactor =3D 1.0;
+                translationCoor =3D [0,0]; break;
+            case "+":
+                scaleFactor *=3D 1.1; break;
+            case "-":
+                scaleFactor *=3D 0.9; break;
+            default:
+                if (typeof zoomParams =3D=3D=3D "number") {
+                    scaleFactor =3D zoomParams;
+                } else if (d3.event !=3D=3D null) {
+                    scaleFactor =3D d3.event.scale;
+                }
+        }
+        if (scaleFactor < self.MIN_SCALE || scaleFactor > self.MAX_SCALE) =
{ return;}
+        self.zoomFunc.scale(scaleFactor); //update scale Factor
+        zoomStatement =3D "translate(" +  self.margins[3] + "," + self.mar=
gins[0] + ")" +
+            " scale(" + scaleFactor + ")";
+
+        // Do manual translation.
+        if( d3.event !=3D=3D null) {
+            translateStatement =3D "translate(" + d3.event.translate + ")";
+        } else {
+            if(typeof translateParams !=3D=3D "undefined") {
+                var x =3D translateParams.split(",")[0];
+                var y =3D translateParams.split(",")[1];
+                if (!isNaN(x) && !isNaN(y)){
+                    translationCoor =3D [translationCoor[0] + parseFloat(x=
), translationCoor[1] + parseFloat(y)];
+                }
+            }
+            self.zoomFunc.translate(translationCoor);   // update zoomFunc
+            translateStatement =3D "translate(" + translationCoor + ")";
+        }
+
+        self.phyloTree.set("scaleFactor", scaleFactor);
+        self.phyloTree.set("translate", translationCoor);
+        self.vis.attr("transform", translateStatement + zoomStatement); //=
refers to the view that we are actually zooming
+    },
+
+
+    reloadViz : function() {
+        /**
+         * Primes the Ajax URL to load another Nexus tree
+         */
+        var self =3D this,
+            treeIndex =3D $("#phylovizNexSelector :selected").val(),
+            dataset_id =3D self.phyloTree.get("dataset_id"),
+            url =3D "phyloviz/getJsonData?dataset_id=3D" + dataset_id + "&=
treeIndex=3D" + String(treeIndex);
+        $.getJSON(url, function(packedJson){
+            window.initPhyloViz(packedJson.data, packedJson.config);
+        });
+    }
+});
+
+
+var HeaderButtons =3D Backbone.View.extend({
+
+    initialize : function(phylovizView){
+        var self =3D this;
+        self.phylovizView =3D phylovizView;
+
+        // Clean up code - if the class initialized more than once
+        $("#panelHeaderRightBtns").empty();
+        $("#phyloVizNavBtns").empty();
+        $("#phylovizNexSelector").off();
+
+        self.initNavBtns();
+        self.initRightHeaderBtns();
+
+        // Initial a tree selector in the case of nexus
+        $("#phylovizNexSelector").off().on("change",  function() {self.phy=
lovizView.reloadViz();}  );
+
+    },
+
+    initRightHeaderBtns : function(){
+        var self =3D this;
+
+        rightMenu =3D create_icon_buttons_menu([
+            { icon_class: 'gear', title: 'PhyloViz Settings', on_click: fu=
nction(){
+                $("#SettingsMenu").show();
+                self.settingsMenu.updateUI();
+            } },
+            { icon_class: 'disk', title: 'Save visualization', on_click: f=
unction() {
+                var nexSelected =3D $("#phylovizNexSelector option:selecte=
d").text();
+                if(nexSelected) {
+                    self.phylovizView.phyloTree.set("title", nexSelected);
+                }
+                self.phylovizView.phyloTree.save();
+            } },
+            { icon_class: 'chevron-expand', title: 'Search / Edit Nodes', =
on_click: function() {
+                $("#nodeSelectionView").show();
+            } },
+            { icon_class: 'information', title: 'Phyloviz Help', on_click:=
 function() {
+                window.open('http://wiki.g2.bx.psu.edu/Learn/Visualization=
/PhylogeneticTree');
+                // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs=
3EyMe1B1X_KFPouzIgrCz3zk/edit
+            } }
+        ],
+            {
+                tooltip_config: { placement: 'bottom' }
+            });
+        $("#panelHeaderRightBtns").append(rightMenu.$el);
+    },
+
+    initNavBtns: function() {
+        var self =3D this,
+            navMenu =3D create_icon_buttons_menu([
+                { icon_class: 'zoom-in', title: 'Zoom in', on_click: funct=
ion() {
+                    self.phylovizView.zoomAndPan({ zoom : "+"});
+                } },
+                { icon_class: 'zoom-out', title: 'Zoom out', on_click: fun=
ction() {
+                    self.phylovizView.zoomAndPan({ zoom : "-"});
+                } },
+                { icon_class: 'arrow-circle', title: 'Reset Zoom/Pan', on_=
click: function() {
+                    self.phylovizView.zoomAndPan({ zoom : "reset"});
+                } }
+            ],
+                {
+                    tooltip_config: { placement: 'bottom' }
+                });
+        $("#phyloVizNavBtns").append(navMenu.$el);
+    }
+});
+
+
+var SettingsMenu =3D UserMenuBase.extend({
+
+    className: 'Settings',
+
+    initialize: function(options){
+        // settings needs to directly interact with the phyloviz model so =
it will get access to it.
+        var self =3D this;
+        self.phyloTree =3D options.phyloTree;
+        self.el =3D $("#SettingsMenu");
+        self.inputs =3D {
+            separation : $("#phyloVizTreeSeparation"),
+            leafHeight : $("#phyloVizTreeLeafHeight"),
+            fontSize   : $("#phyloVizTreeFontSize")
+        };
+
+        //init all buttons of settings
+        $("#settingsCloseBtn").off().on("click", function() { self.el.hide=
(); });
+        $("#phylovizResetSettingsBtn").off().on("click", function() { self=
.resetToDefaults(); });
+        $("#phylovizApplySettingsBtn").off().on("click", function() { self=
.apply(); });
+    },
+
+    apply : function(){
+        /**
+         * Applying user values to phylotree model.
+         */
+        var self =3D this;
+        if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) ||
+            !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) ||
+            !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){
+            return;
+        }
+        $.each(self.inputs, function(key, $input){
+            self.phyloTree.set(key, $input.val());
+        });
+    },
+    updateUI : function(){
+        /**
+         * Called to update the values input to that stored in the model
+         */
+        var self =3D this;
+        $.each(self.inputs, function(key, $input){
+            $input.val(self.phyloTree.get(key));
+        });
+    },
+    resetToDefaults : function(){
+        /**
+         * Resets the value of the phyloTree model to its default
+         */
+        $(".bs-tooltip").remove();      // just in case the tool tip was n=
ot removed
+        var self =3D this;
+        $.each(self.phyloTree.defaults, function(key, value) {
+            self.phyloTree.set(key, value);
+        });
+        self.updateUI();
+    },
+
+    render: function(){
+
+    }
+
+});
+
+
+var NodeSelectionView =3D UserMenuBase.extend({
+    /**
+     * View for inspecting node properties and editing them
+     */
+    className: 'Settings',
+
+    initialize : function (options){
+        var self =3D this;
+        self.el =3D $("#nodeSelectionView");
+        self.phyloTree =3D options.phyloTree;
+
+        self.UI =3D {
+            enableEdit      : $('#phylovizEditNodesCheck'),
+            saveChanges     : $('#phylovizNodeSaveChanges'),
+            cancelChanges   : $("#phylovizNodeCancelChanges"),
+            name            : $("#phyloVizSelectedNodeName"),
+            dist            : $("#phyloVizSelectedNodeDist"),
+            annotation      : $("#phyloVizSelectedNodeAnnotation")
+        };
+
+        self.valuesOfConcern =3D {
+            name : null,
+            dist : null,
+            annotation : null
+        }; // temporarily stores the values in case user change their mind
+
+        //init UI buttons
+        $("#nodeSelCloseBtn").off().on("click", function() { self.el.hide(=
); });
+        self.UI.saveChanges.off().on("click", function(){ self.updateNodes=
(); });
+        self.UI.cancelChanges.off().on("click", function(){ self.cancelCha=
nges(); });
+
+        (function ($) {
+            // extending jquery fxn for enabling and disabling nodes.
+            $.fn.enable =3D function (isEnabled) {
+                return $(this).each(function () {
+                    if(isEnabled){
+                        $(this).removeAttr('disabled');
+                    } else {
+                        $(this).attr('disabled', 'disabled');
+                    }
+                });
+            };
+        })(jQuery);
+
+        self.UI.enableEdit.off().on("click", function () {
+            self.toggleUI();
+        });
+    },
+
+    toggleUI : function(){
+        /**
+         * For turning on and off the child elements
+         */
+        var self =3D this,
+            checked =3D self.UI.enableEdit.is(':checked');
+
+        !checked ? self.cancelChanges() : "";
+
+        $.each(self.valuesOfConcern, function(key, value) {
+            self.UI[key].enable(checked);
+        });
+        if(checked){
+            self.UI.saveChanges.show();
+            self.UI.cancelChanges.show();
+        } else {
+            self.UI.saveChanges.hide();
+            self.UI.cancelChanges.hide();
+        }
+
+    },
+
+    cancelChanges : function() {
+        /**
+         * Reverting to previous values in case user change their minds
+         */
+        var self =3D this,
+            node =3D self.phyloTree.get("selectedNode");
+        if (node){
+            $.each(self.valuesOfConcern, function(key, value) {
+                self.UI[key].val(node[key]);
+            });
+        }
+    },
+
+    updateNodes : function (){
+        /**
+         * Changing the data in the underlying tree with user-specified va=
lues
+         */
+        var self =3D this,
+            node =3D self.phyloTree.get("selectedNode");
+        if (node){
+            if (!self.isAcceptableValue(self.UI.dist, 0, 1) ||
+                self.hasIllegalJsonCharacters(self.UI.name) ||
+                self.hasIllegalJsonCharacters(self.UI.annotation) ) {
+                return;
+            }
+            $.each(self.valuesOfConcern, function(key, value) {
+                (node[key]) =3D self.UI[key].val();
+            });
+            self.phyloTree.set("nodeAttrChangedTime", new Date());
+        } else {
+            alert("No node selected");
+        }
+    }
+
+
+});
+
+
+
+var PhyloVizSearch =3D UserMenuBase.extend({
+    /**
+     * Initializes the search panel on phyloviz and handles its user inter=
action
+     * It allows user to search the entire free based on some qualifer, li=
ke dist <=3D val.
+     */
+    initialize : function () {
+        var self =3D this;
+
+        $("#phyloVizSearchBtn").on("click", function(){
+            var searchTerm =3D $("#phyloVizSearchTerm"),
+                searchConditionVal =3D $("#phyloVizSearchCondition").val()=
.split("-"),
+                attr =3D searchConditionVal[0],
+                condition =3D searchConditionVal[1];
+            self.hasIllegalJsonCharacters(searchTerm);
+
+            if (attr =3D=3D=3D "dist"){
+                self.isAcceptableValue(searchTerm, 0, 1);
+            }
+            self.searchTree(attr, condition, searchTerm.val());
+        });
+    },
+
+    searchTree : function (attr, condition, val){
+        /**
+         * Searches the entire tree and will highlight the nodes that matc=
h the condition in green
+         */
+        d3.selectAll("g.node")
+            .classed("searchHighlight", function(d){
+                var attrVal =3D  d[attr];
+                if (typeof attrVal !=3D=3D "undefined" && attrVal !=3D=3D =
null){
+                    if (attr =3D=3D=3D "dist"){
+                        switch (condition) {
+                            case "greaterEqual":
+                                return attrVal >=3D +val;
+                            case "lesserEqual":
+                                return attrVal <=3D +val;
+                            default:
+                                return;
+                        }
+
+                    } else if (attr =3D=3D=3D "name" || attr =3D=3D=3D "an=
notation") {
+                        return attrVal.toLowerCase().indexOf(val.toLowerCa=
se()) !=3D=3D -1;
+                    }
+                }
+            });
+    }
+});
\ No newline at end of file


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 templates/root/history.mako
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -272,6 +272,17 @@
     }
    =20
     init_trackster_links();
+
+    function init_phyloviz_links() {
+        // PhyloViz links
+        // Add to trackster browser functionality
+        $(".phyloviz-add").live("click", function() {
+            var dataset =3D this,
+                    dataset_jquery =3D $(this);
+            window.parent.location =3D dataset_jquery.attr("new-url");
+        });
+    }
+    init_phyloviz_links();
    =20
     // History rename functionality.
     async_save_text("history-name-container", "history-name", "${h.url_for=
( controller=3D"/history", action=3D"rename_async", id=3Dtrans.security.enc=
ode_id(history.id) )}", "new_name", 18);


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 templates/root/history_common.mako
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -29,6 +29,9 @@
 ## Render the dataset `data` as history item, using `hid` as the displayed=
 id
 <%def name=3D"render_dataset( data, hid, show_deleted_on_refresh =3D False=
, for_editing =3D True, display_structured =3D False )"><%
+
+        from galaxy.datatypes.xml import Phyloxml
+        from galaxy.datatypes.data import Newick, Nexus
         dataset_id =3D trans.security.encode_id( data.id )
=20
         if data.state in ['no state','',None]:
@@ -230,6 +233,14 @@
                                 action-url=3D"${h.url_for( controller=3D't=
racks', action=3D'browser', dataset_id=3Ddataset_id)}"
                                 new-url=3D"${h.url_for( controller=3D'trac=
ks', action=3D'index', dataset_id=3Ddataset_id, default_dbkey=3Ddata.dbkey)=
}" title=3D"View in Trackster"></a>
                         %endif
+                        <%
+                            isPhylogenyData =3D isinstance(data.datatype, =
 (Phyloxml, Nexus, Newick))
+                        %>
+                        %if isPhylogenyData:
+                                <a href=3D"javascript:void(0)"  class=3D"i=
con-button chart_curve phyloviz-add"
+                                   action-url=3D"${h.url_for( controller=
=3D'phyloviz', action=3D'-', dataset_id=3Ddataset_id)}"
+                                   new-url=3D"${h.url_for( controller=3D'p=
hyloviz', action=3D'index', dataset_id=3Ddataset_id)}" title=3D"View in Phy=
loviz"></a>
+                        %endif
                         %if trans.user:
                             %if not display_structured:
                                 <div style=3D"float: right">


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 templates/visualization/phyloviz.mako
--- /dev/null
+++ b/templates/visualization/phyloviz.mako
@@ -0,0 +1,320 @@
+<%inherit file=3D"/webapps/galaxy/base_panels.mako"/>
+##
+<%def name=3D"init()">
+    <%
+        self.has_left_panel=3DFalse
+        self.has_right_panel=3DFalse
+        self.active_view=3D"visualization"
+        self.message_box_visible=3DFalse
+    %>
+</%def>
+
+<%def name=3D"stylesheets()">
+    ${parent.stylesheets()}
+    <style>
+
+        .node circle {
+            cursor: pointer;
+            fill: #fff;
+            stroke: steelblue;
+            stroke-width: 1.5px;
+        }
+
+        .node.searchHighlight circle {
+            stroke-width: 3px;
+            stroke: #7adc26;
+        }
+
+        .node.selectedHighlight circle {
+            stroke-width: 3px;
+            stroke: #dc143c;
+        }
+
+        path.link {
+            fill: none;
+            stroke: #B5BBFF;
+            stroke-width: 4.0px;
+        }
+
+
+        div #phyloVizNavContainer{
+            text-align: center;
+            width: 100%;
+            height: 0px;
+        }
+
+        div #phyloVizNav{
+            font-weight: bold;
+            display: inline-block;
+            background: transparent;
+            top: -2em;
+            position: relative;
+        }
+
+        div .navControl{
+            float: left;
+        }
+
+        div#FloatingMenu {
+            left: 0;
+            top: 15%;
+            width:20%;
+            z-index:100;
+            padding: 5px;
+
+        }
+
+        div#SettingsMenu {
+            width: 25%;
+            top: 350px;
+
+        }
+
+        div#nodeSelectionView {
+            width: 25%;
+            top:70px;
+        }
+
+        .Panel {
+            right: 0%;
+            z-index: 101;
+            position: fixed;
+
+        ##          Borrowed from galaxy modal_dialogues
+                    background-color: white;
+            border: 1px solid #999;
+            border: 1px solid rgba(0, 0, 0, 0.3);
+            -webkit-border-radius: 6px;
+            -moz-border-radius: 6px;
+            border-radius: 6px;
+            -webkit-border-radius: 6px;
+            -moz-border-radius: 6px;
+            border-radius: 6px;
+            -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+            -webkit-background-clip: padding-box;
+            -moz-background-clip: padding-box;
+            background-clip: padding-box;
+            -webkit-background-clip: padding-box;
+            -moz-background-clip: padding-box;
+            background-clip: padding-box;
+        }
+
+        span.PhylovizCloseBtn{
+            cursor: pointer;
+            float : right;
+        }
+
+        #PhyloViz{
+            width: 100%;
+            height: 95%;
+        }
+
+        h2.PhyloVizMenuTitle{
+            color: white;
+        }
+
+        ##        Settings Menu
+        .SettingMenuRows{
+                    margin: 2px 0 2px 0;
+                }
+
+
+        ##        Helper Styles
+        .PhyloVizFloatLeft{
+                    float : left;
+                }
+        .icon-button.zoom-in,.icon-button.zoom-out{display:inline-block;he=
ight:16px;width:16px;margin-bottom:-3px;cursor:pointer;}
+        .icon-button.zoom-out{background:transparent url(../images/fugue/m=
agnifier-zoom-out.png) center center no-repeat;}
+        .icon-button.zoom-in{margin-left:10px;background:transparent url(.=
./images/fugue/magnifier-zoom.png) center center no-repeat;}
+
+    </style>
+</%def>
+
+
+<%def name=3D"javascripts()">
+    ${parent.javascripts()}
+    ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "=
viz/phyloviz")}
+</%def>
+
+
+
+<%def name=3D"center_panel()">
+
+    <div class=3D"unified-panel-header" unselectable=3D"on">
+        <div class=3D"unified-panel-header-inner">
+            <div style=3D"float:left;" id=3D"title"></div>
+            <div style=3D"float:right;" id=3D"panelHeaderRightBtns"></div>
+        </div>
+        <div style=3D"clear: both"></div>
+    </div>
+
+
+    <div id=3D"phyloVizNavContainer">
+        <div id=3D"phyloVizNav">
+            %if config["ext"] =3D=3D "nex" and not config["saved_visualiza=
tion"]:
+                <div id =3D "phylovizNexInfo" class=3D"navControl">
+                <p>Select a tree to view:   
+                <select id=3D"phylovizNexSelector">
+                    % for tree, index in config["trees"]:
+                        <option value=3D"${index}">${tree}</option>
+                    % endfor
+                </select>
+                </p>
+                </div>
+            %endif
+            <div id=3D"phyloVizNavBtns" class=3D"navControl">
+            </div>
+            <div class=3D"navControl">
+                <p> | Alt+click to select nodes</p>
+            </div>
+
+
+        </div>
+
+    </div>
+
+    ##  Node Selection Menu
+    <div id=3D"nodeSelectionView" class=3D"Panel">
+        <div class=3D"modal-header">
+            <h3 class=3D"PhyloVizMenuTitle">Search / Edit Nodes :
+                <span class=3D"PhylovizCloseBtn" id=3D"nodeSelCloseBtn"> X=
 </span>
+            </h3>
+        </div>
+
+        <div class=3D"modal-body">
+
+            <div class=3D"SettingMenuRows">
+                Search for nodes with:
+                <select id=3D"phyloVizSearchCondition" style=3D"width: 55%=
">
+                    <option value=3D"name-containing">Name (containing)</o=
ption>
+                    <option value=3D"annotation-containing">Annotation (co=
ntaining)</option>
+                    <option value=3D"dist-greaterEqual">Distance (>=3D)</o=
ption>
+                    <option value=3D"dist-lesserEqual">Distance (<=3D)</op=
tion>
+                </select>
+                <input  type=3D"text" id=3D"phyloVizSearchTerm" value=3D"N=
one" size=3D"15" displayLabel=3D"Distance">
+
+                <div class=3D"SettingMenuRows" style=3D"text-align: center=
;">
+                    <button id=3D"phyloVizSearchBtn" > Search! </button>
+                </div>
+            </div>
+
+            <br/>
+
+            <div class=3D"SettingMenuRows">
+                Name: <input type=3D"text" id=3D"phyloVizSelectedNodeName"=
 value=3D"None" size=3D"15" disabled=3D"disabled" >
+            </div>
+            <div class=3D"SettingMenuRows">
+                Dist: <input type=3D"text" id=3D"phyloVizSelectedNodeDist"=
 value=3D"None" size=3D"15" disabled=3D"disabled" displayLabel=3D"Distance">
+            </div>
+            <div class=3D"SettingMenuRows">
+                Annotation:
+                <textarea id=3D"phyloVizSelectedNodeAnnotation" disabled=
=3D"disabled" ></textarea>
+            </div>
+            <div class=3D"SettingMenuRows">
+                Edit: <input type=3D"checkbox" id=3D"phylovizEditNodesChec=
k" value=3D"You can put custom annotations here and it will be saved">
+                <button id=3D"phylovizNodeSaveChanges" style=3D"display: n=
one;"> Save edits</button>
+                <button id=3D"phylovizNodeCancelChanges" style=3D"display:=
 none;"> Cancel</button>
+            </div>
+        </div>
+    </div>
+
+    ##  Settings Menus
+    <div id=3D"SettingsMenu" class=3D"Panel">
+        <div class=3D"modal-header">
+            <h3 class=3D"PhyloVizMenuTitle">Phyloviz Settings:
+                <span class=3D"PhylovizCloseBtn" id=3D"settingsCloseBtn"> =
X </span>
+            </h3>
+        </div>
+        <div class=3D"modal-body">
+            <div class=3D"SettingMenuRows">
+                Phylogenetic Spacing (px per unit): <input id=3D"phyloVizT=
reeSeparation" type=3D"text" value=3D"250" size=3D"10" displayLabel=3D"Phyl=
ogenetic Separation"> (50-2500)
+            </div>
+            <div class=3D"SettingMenuRows">
+                Vertical Spacing (px): <input type=3D"text" id=3D"phyloViz=
TreeLeafHeight" value=3D"18" size=3D"10" displayLabel=3D"Vertical Spacing">=
 (5-30)
+            </div>
+            <div class=3D"SettingMenuRows">
+                Font Size (px): <input type=3D"text" id=3D"phyloVizTreeFon=
tSize" value=3D"12" size=3D"4" displayLabel=3D"Font Size"> (5-20)
+            </div>
+
+        </div>
+        <div class=3D"modal-footer">
+            <button id=3D"phylovizResetSettingsBtn" class=3D"PhyloVizFloat=
Left" > Reset </button>
+            <button id=3D"phylovizApplySettingsBtn" class=3D"PhyloVizFloat=
Right" > Apply </button>
+        </div>
+    </div>
+
+
+
+
+
+
+    <div class=3D"Panel" id=3D"FloatingMenu" style=3D"display: None;">
+
+        <h2>PhyloViz (<a onclick=3D"displayHelp()" href=3D"javascript:void=
(0);">?</a>)</h2>
+        <div style=3D"display: none;">
+            <h2>Summary of Interactions and Functions:</h2>
+            <div class=3D"hint">1. Expansion of Nodes: click or option-cli=
ck to expand or collapse</div>
+            <div class=3D"hint">2. Zooming and translation: mousewheel, bu=
ttons, click and drag, double click. Reset</div>
+            <div class=3D"hint">3. Tooltip: Displays "Name and Size" on mo=
useOver on nodes</div>
+            <div class=3D"hint">4. Minimap: Currently displays an exact bu=
t scaled down replicate of the tree, orange bounding box is correct for lin=
ear only<br/>
+                Can be switched on or off</div>
+            <div class=3D"hint">5. Changing Layouts: Able to change betwee=
n circular and linear layouts.</div>
+
+        </div>
+
+        <h5>Scaling & Rotation:</h5>
+        <button id=3D"phylovizZoomInBtn" class=3D"" > + </button>
+        <button id=3D"phylovizZoomOutBtn" class=3D"" > - </button>
+
+
+        <h5>Translation:</h5>
+        <button id=3D"phylovizTranslateUpBtn" > Up </button>
+        <button id=3D"phylovizTranslateDownBtn" > Down </button>
+        <br/>
+        <button id=3D"phylovizTranslateLeftBtn" > Left </button>
+        <button id=3D"phylovizTranslateRightBtn" > Right </button>
+
+
+
+        <h5>Others:</h5>
+        <button id=3D"phylovizResetBtn" > Reset Zoom/Translate </button>
+        <button id=3D"phylovizSaveBtn" > Save vizualization </button>
+        <button id=3D"phylovizOpenSettingsBtn" > Settings </button>
+    </div>
+
+    <div id=3D"PhyloViz" >
+    </div>
+
+    <script type=3D"text/javascript">
+
+        function initPhyloViz(data, config) {
+            var phyloviz;
+
+            // -- Initialization code |-->
+            phyloviz =3D new PhylovizView({
+                data: data,
+                layout : "Linear",
+                config :  config
+            });
+
+            // -- Render viz. --
+            phyloviz.render();
+
+        }
+
+        $(function firstVizLoad(){       // calls when viz is loaded for t=
he first time
+            var config =3D JSON.parse( '${ h.to_json_string( config )}');
+            var data =3D JSON.parse('${h.to_json_string(data)}');
+            initPhyloViz(data, config);
+        });
+
+    </script>
+
+</%def>
+
+


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 test-data/visualization/phyloviz/1_nexus.nex
--- /dev/null
+++ b/test-data/visualization/phyloviz/1_nexus.nex
@@ -0,0 +1,87 @@
+#NEXUS
+
+[!This data set was downloaded from TreeBASE, a relational database of phy=
logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer=
sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl=
edgment from the Nexus file.
+
+
+Generated on June 12, 2012; 23:00 GMT
+
+TreeBASE (cc) 1994-2008
+
+Study reference:
+Olariaga I., Grebenc T., Salcedo I., & Mart=C3=ADn M.P. 2012. Two new spec=
ies of Hydnum
+with ovoid basidiospores: H. ovoideisporum and H. vesterholtii. Mycologia,=
 .
+
+TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S128=
31]
+
+BEGIN TREES;
+      TITLE Hydnum_ITS_result;
+      LINK TAXA =3D Taxa1;
+         TRANSLATE
+            1    Hydnum_aff_ellipsosporum_RUFHYD1_AJ535304,
+            2    Hydnum_albidum_ALB_AY817135,
+            3    Hydnum_albidum_ALBHYD1_AJ534974,
+            4    Hydnum_albomagnum_ALM_DQ218305,
+            5    Hydnum_ellipsosporum_ELL_AY817138,
+            6    Hydnum_ellipsosporum_RUFHYD8_AJ547882,
+            7    Hydnum_ovoidisporum_12317BIOFungi,
+            8    Hydnum_ovoidisporum_12683BIOFungi,
+            9    Hydnum_ovoidisporum_12902BIOFungi,
+            10   Hydnum_ovoidisporum_14130BIOFungi,
+            11   Hydnum_repandum_RE1_REP1_AJ889978,
+            12   Hydnum_repandum_RE1_REP2_AJ889949,
+            13   Hydnum_repandum_RE1_REP3_AY817136,
+            14   Hydnum_repandum_RE1_REP6_UDB000025,
+            15   Hydnum_repandum_RE1_REP7_UDB000096,
+            16   Hydnum_repandum_RE1_REP8_UDB001479,
+            17   Hydnum_repandum_RE1_REPHYD10_AJ547888,
+            18   Hydnum_repandum_RE1_REPHYD11_AJ547886,
+            19   Hydnum_repandum_RE1_REPHYD1_AJ547871,
+            20   Hydnum_repandum_RE1_REPHYD3_AJ547874,
+            21   Hydnum_repandum_RE1_REPHYD4_AJ547876,
+            22   Hydnum_repandum_RE1_REPHYD5_AJ547875,
+            23   Hydnum_repandum_RE1_REPHYD6_AJ547877,
+            24   Hydnum_repandum_RE1_REPHYD7_AJ547878,
+            25   Hydnum_repandum_RE1_REPHYD8_AJ547881,
+            26   Hydnum_repandum_RE1_REPHYD9_AJ547883,
+            27   Hydnum_repandum_RE1_RUFHYD10_AJ547866,
+            28   Hydnum_repandum_RE1_RUFHYD11_AJ547889,
+            29   Hydnum_repandum_RE1_RUFHYD9_AJ535305,
+            30   Hydnum_rufescens_RU1_RUFHYD5_AJ547869,
+            31   Hydnum_rufescens_RU1_RUFHYD6_AJ547884,
+            32   Hydnum_rufescens_RU1_RUFHYD7_AJ547870,
+            33   Hydnum_rufescens_RU2_REP5_DQ367902,
+            34   Hydnum_rufescens_RU2_RUFHYD2_AJ535301,
+            35   Hydnum_rufescens_RU3_12901BIOFungi,
+            36   Hydnum_rufescens_RU3_REP4_DQ218306,
+            37   Hydnum_rufescens_RU3_RUFHYD3_AJ535303,
+            38   Hydnum_rufescens_RU3_RUFHYD4_AJ535302,
+            39   Hydnum_rufescens_RU4_RUFHYD12_AJ839969,
+            40   Hydnum_rufescens_RU4_RUFHYD16_AJ547868,
+            41   Hydnum_rufescens_RU4_RUFHYD17_AJ547885,
+            42   Hydnum_rufescens_RU4_UMB1_DQ367903,
+            43   Hydnum_rufescens_RU5_12760BIOFungi,
+            44   Hydnum_rufescens_RU5_ALBHYD2_AJ534975,
+            45   Hydnum_rufescens_RU5_RUF2_DQ658890,
+            46   Hydnum_rufescens_RU5_RUF4_UDB001465,
+            47   Hydnum_rufescens_RU5_RUF5_UDB002423,
+            48   Hydnum_rufescens_RU5_RUFHYD14_AJ547872,
+            49   Hydnum_rufescens_RU6_RUF1_AY817137,
+            50   Hydnum_rufescens_RU6_RUFHYD15_AJ547867,
+            51   Hydnum_rufescens_wrong_taxonomy_RUF3_AM087246,
+            52   Hydnum_umbilicatum_UMBHYD1_AJ534972,
+            53   Hydnum_umbilicatum_UMBHYD2_AJ534973,
+            54   Hydnum_vesterholtii_10429BIOFungi,
+            55   Hydnum_vesterholtii_10452BIOFungi,
+            56   Hydnum_vesterholtii_12330BIOFungi,
+            57   Hydnum_vesterholtii_12904BIOFungi,
+            58   Hydnum_vesterholtii_REPHYD12A_AJ547879,
+            59   Hydnum_vesterholtii_REPHYD12C_AJ783968,
+            60   Hydnum_vesterholtii_REPHYD13_AJ547887,
+            61   Sistotrema_muscicola_AJ606040,
+            62   Sistotrema_alboluteum_AJ606042;
+      TREE Fig._2 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66=
,((4:100.0,(2:100.0,3:100.0):100.0):60.639999,(((56:100.0,58:100.0,59:100.0=
):84.639999,(54:100.0,55:100.0,57:100.0,60:100.0):98.330002):92.5,(((30:100=
.0,31:100.0,32:100.0):100.0,(11:100.0,12:100.0,13:100.0,14:100.0,15:100.0,1=
6:100.0,17:100.0,18:100.0,19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,24:1=
00.0,25:100.0,26:100.0):99.93):68.690002,(((33:100.0,34:100.0):49.8050005,(=
35:100.0,36:100.0,37:100.0,38:100.0):99.989998):49.8050005,((7:100.0,8:100.=
0,9:100.0,10:100.0):100.0,(42:100.0,(39:100.0,40:100.0,41:100.0):98.449997)=
:86.790001,((52:100.0,53:100.0):99.93,(1:100.0,(5:97.47999949999999,6:100.0=
):97.47999949999999):100.0):53.310001,(27:100.0,(28:100.0,29:100.0,49:100.0=
,50:100.0):47.404999):47.404999,(43:100.0,44:100.0,45:100.0,46:100.0,47:100=
.0,48:100.0):99.459999):29.245001):29.245001):51.580002):61.540001):49.66);
+      TREE PAUP_1 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66=
,((4:100.0,(3:100.0,2:100.0):100.0):60.639999,(((58:100.0,59:100.0,56:100.0=
):84.639999,(60:100.0,54:100.0,55:100.0,57:100.0):98.330002):92.5,(((30:100=
.0,31:100.0,32:100.0):100.0,(19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,2=
4:100.0,25:100.0,26:100.0,17:100.0,18:100.0,11:100.0,12:100.0,13:100.0,14:1=
00.0,15:100.0,16:100.0):99.93):68.690002,((34:100.0,33:100.0):99.610001,(37=
:100.0,38:100.0,35:100.0,36:100.0):99.989998,(42:100.0,(39:100.0,41:100.0,4=
0:100.0):98.449997):86.790001,(8:100.0,7:100.0,9:100.0,10:100.0):100.0,((52=
:100.0,53:100.0):99.93,(1:100.0,(5:100.0,6:100.0):94.959999):100.0):53.3100=
01,(29:100.0,27:100.0,28:100.0,50:100.0,49:100.0):94.809998,(44:100.0,43:10=
0.0,48:100.0,45:100.0,46:100.0,47:100.0):99.459999):58.490002):51.580002):6=
1.540001):49.66);
+
+
+
+END;


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 test-data/visualization/phyloviz/2_nexus.nex
--- /dev/null
+++ b/test-data/visualization/phyloviz/2_nexus.nex
@@ -0,0 +1,96 @@
+#NEXUS
+
+[!This data set was downloaded from TreeBASE, a relational database of phy=
logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer=
sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl=
edgment from the Nexus file.
+
+
+Generated on August 18, 2012; 12:14 GMT
+
+TreeBASE (cc) 1994-2008
+
+Study reference:
+Naish D., Dyke G., Cau A., & Escuilli=C3=A9 F. 2012. A gigantic bird from =
the Upper Cretaceous
+of Central Asia. Biology Letters, 8(1): 97-100.
+
+TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S130=
08]
+
+BEGIN TREES;
+      TITLE Imported_trees;
+      LINK TAXA =3D Taxa1;
+         TRANSLATE
+            1    Herrerasaurus,
+            2    Tawa,
+            3    Allosaurus,
+            4    Alvarezsaurus,
+            5    Anchiornis,
+            6    Archaeopteryx,
+            7    Archaeorhynchus,
+            8    Avimimus,
+            9    Baryonyx,
+            10   Beipiaosaurus,
+            11   Caenagnathus,
+            12   Caudipteryx,
+            13   Ceratosaurus,
+            14   Chirostenotes,
+            15   Citipati,
+            16   Compsognathus,
+            17   Confuciusornis,
+            18   Dilong,
+            19   Dilophosaurus,
+            20   Epidendrosaurus,
+            21   Epidexipteryx,
+            22   Erlicosaurus,
+            23   Eustreptospondylus,
+            24   Gallimimus,
+            25   Garudimimus,
+            26   Gobipteryx,
+            27   Guanlong,
+            28   Haplocheirus,
+            29   Harpymimus,
+            30   Hebeiornis,
+            31   Hongshanornis,
+            32   Huoshanornis,
+            33   Iberomesornis,
+            34   Ichthyornis,
+            35   Incisivosaurus,
+            36   Jeholornis,
+            37   Limusaurus,
+            38   Longicrusavis,
+            39   Longipteryx,
+            40   Longirostravis,
+            41   Majungasaurus,
+            42   Masiakasaurus,
+            43   Monolophosaurus,
+            44   Mononykus,
+            45   Neornithes,
+            46   Ornitholestes,
+            47   Ornithomimus,
+            48   Patagonykus,
+            49   Patagopteryx,
+            50   Pelecanimimus,
+            51   Pengornis,
+            52   Protarchaeopteryx,
+            53   Protopteryx,
+            54   Rinchenia,
+            55   Sapeornis,
+            56   Segnosaurus,
+            57   Shenzhousaurus,
+            58   Shuvuuia,
+            59   Sinornithosaurus,
+            60   Sinosauropteryx,
+            61   Sinovenator,
+            62   Sinraptor,
+            63   Syntarsus_kayentakatae,
+            64   Troodon,
+            65   Tyrannosaurus,
+            66   Velociraptor,
+            67   Yanornis,
+            68   Yixianornis,
+            69   Zhongjianornis,
+            70   Zhongornis,
+            71   Zuolong,
+            72   Samrukia;
+      TREE Figure_1A =3D [&R] (1,(2,(((((43,(3,62)),(71,((46,((((28,(4,(48=
,(44,58)))),((((5,(61,(64,(59,66)))),(6,((36,(55,(69,(((7,34,45,49,72,(31,3=
8),(67,68)),(33,((32,((26,30),(39,40))),(51,53)))),(17,70))))),(20,21)))),(=
(11,(12,(8,(14,(15,54))))),(35,52))),(10,(22,56)))),(50,(57,(29,(25,(24,47)=
))))),(16,60))),(27,(18,65))))),(9,23)),(13,(41,(37,42)))),(19,63))));
+
+
+
+END;


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 test-data/visualization/phyloviz/3_phyloxml.xml
--- /dev/null
+++ b/test-data/visualization/phyloviz/3_phyloxml.xml
@@ -0,0 +1,257 @@
+<?xml version=3D"1.0" encoding=3D"UTF-8"?>
+<phyloxml xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance"
+   xsi:schemaLocation=3D"http://www.phyloxml.org http://www.phyloxml.org/1=
.10/phyloxml.xsd"
+   xmlns=3D"http://www.phyloxml.org">
+   <phylogeny rooted=3D"true">
+      <clade>
+         <clade>
+            <branch_length>0.18105</branch_length>
+            <confidence type=3D"unknown">89.0</confidence>
+            <clade>
+               <branch_length>0.07466</branch_length>
+               <confidence type=3D"unknown">32.0</confidence>
+               <clade>
+                  <branch_length>0.26168</branch_length>
+                  <confidence type=3D"unknown">100.0</confidence>
+                  <clade>
+                     <branch_length>0.22058</branch_length>
+                     <confidence type=3D"unknown">89.0</confidence>
+                     <clade>
+                        <branch_length>0.28901</branch_length>
+                        <confidence type=3D"unknown">100.0</confidence>
+                        <clade>
+                           <branch_length>0.06584</branch_length>
+                           <confidence type=3D"unknown">100.0</confidence>
+                           <clade>
+                              <branch_length>0.02309</branch_length>
+                              <confidence type=3D"unknown">43.0</confidenc=
e>
+                              <clade>
+                                 <branch_length>0.0746</branch_length>
+                                 <confidence type=3D"unknown">100.0</confi=
dence>
+                                 <clade>
+                                    <branch_length>0.02365</branch_length>
+                                    <confidence type=3D"unknown">88.0</con=
fidence>
+                                    <clade>
+                                       <name>22_MOUSE</name>
+                                       <branch_length>0.05998</branch_leng=
th>
+                                       <taxonomy>
+                                          <code>MOUSE</code>
+                                       </taxonomy>
+                                    </clade>
+                                    <clade>
+                                       <name>Apaf-1_HUMAN</name>
+                                       <branch_length>0.01825</branch_leng=
th>
+                                       <taxonomy>
+                                          <code>HUMAN</code>
+                                       </taxonomy>
+                                    </clade>
+                                 </clade>
+                                 <clade>
+                                    <name>12_CANFA</name>
+                                    <branch_length>0.04683</branch_length>
+                                    <taxonomy>
+                                       <code>CANFA</code>
+                                    </taxonomy>
+                                 </clade>
+                              </clade>
+                              <clade>
+                                 <name>11_CHICK</name>
+                                 <branch_length>0.15226</branch_length>
+                                 <taxonomy>
+                                    <code>CHICK</code>
+                                 </taxonomy>
+                              </clade>
+                           </clade>
+                           <clade>
+                              <name>16_XENLA</name>
+                              <branch_length>0.4409</branch_length>
+                              <taxonomy>
+                                 <code>XENLA</code>
+                              </taxonomy>
+                           </clade>
+                        </clade>
+                        <clade>
+                           <branch_length>0.17031</branch_length>
+                           <confidence type=3D"unknown">100.0</confidence>
+                           <clade>
+                              <branch_length>0.10929</branch_length>
+                              <confidence type=3D"unknown">100.0</confiden=
ce>
+                              <clade>
+                                 <name>14_FUGRU</name>
+                                 <branch_length>0.02255</branch_length>
+                                 <taxonomy>
+                                    <code>FUGRU</code>
+                                 </taxonomy>
+                              </clade>
+                              <clade>
+                                 <name>15_TETNG</name>
+                                 <branch_length>0.09478</branch_length>
+                                 <taxonomy>
+                                    <code>TETNG</code>
+                                 </taxonomy>
+                              </clade>
+                           </clade>
+                           <clade>
+                              <name>17_BRARE</name>
+                              <branch_length>0.1811</branch_length>
+                              <taxonomy>
+                                 <code>BRARE</code>
+                              </taxonomy>
+                           </clade>
+                        </clade>
+                     </clade>
+                     <clade>
+                        <branch_length>0.01594</branch_length>
+                        <confidence type=3D"unknown">53.0</confidence>
+                        <clade>
+                           <branch_length>0.10709</branch_length>
+                           <confidence type=3D"unknown">68.0</confidence>
+                           <clade>
+                              <name>1_BRAFL</name>
+                              <branch_length>0.26131</branch_length>
+                              <taxonomy>
+                                 <code>BRAFL</code>
+                              </taxonomy>
+                           </clade>
+                           <clade>
+                              <name>18_NEMVE</name>
+                              <branch_length>0.38014</branch_length>
+                              <taxonomy>
+                                 <code>NEMVE</code>
+                              </taxonomy>
+                           </clade>
+                        </clade>
+                        <clade>
+                           <name>23_STRPU</name>
+                           <branch_length>0.48179</branch_length>
+                           <taxonomy>
+                              <code>STRPU</code>
+                           </taxonomy>
+                        </clade>
+                     </clade>
+                  </clade>
+                  <clade>
+                     <branch_length>0.34475</branch_length>
+                     <confidence type=3D"unknown">100.0</confidence>
+                     <clade>
+                        <name>26_STRPU</name>
+                        <branch_length>0.36374</branch_length>
+                        <taxonomy>
+                           <code>STRPU</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"1319">
+                              <domain from=3D"18" to=3D"98" confidence=3D"=
3.4E-5">Death</domain>
+                              <domain from=3D"189" to=3D"481" confidence=
=3D"1.8E-10">NB-ARC</domain>
+                              <domain from=3D"630" to=3D"668" confidence=
=3D"8.2E-5">WD40</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                     <clade>
+                        <name>25_STRPU</name>
+                        <branch_length>0.33137</branch_length>
+                        <taxonomy>
+                           <code>STRPU</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"1947">
+                              <domain from=3D"143" to=3D"227" confidence=
=3D"7.4E-5">Death</domain>
+                              <domain from=3D"227" to=3D"550" confidence=
=3D"2.0E-13">NB-ARC</domain>
+                              <domain from=3D"697" to=3D"736" confidence=
=3D"7.9E-4">WD40</domain>
+                              <domain from=3D"745" to=3D"785" confidence=
=3D"1.5">WD40</domain>
+                              <domain from=3D"1741" to=3D"1836" confidence=
=3D"2.0">Adeno_VII</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+               </clade>
+               <clade>
+                  <branch_length>1.31498</branch_length>
+                  <confidence type=3D"unknown">100.0</confidence>
+                  <clade>
+                     <name>CED4_CAEEL</name>
+                     <branch_length>0.13241</branch_length>
+                     <taxonomy>
+                        <code>CAEEL</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length=3D"714">
+                           <domain from=3D"7" to=3D"90" confidence=3D"9.2E=
-14">CARD</domain>
+                           <domain from=3D"116" to=3D"442" confidence=3D"5=
.8E-151">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+                  <clade>
+                     <name>31_CAEBR</name>
+                     <branch_length>0.04777</branch_length>
+                     <taxonomy>
+                        <code>CAEBR</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length=3D"554">
+                           <domain from=3D"1" to=3D"75" confidence=3D"0.00=
46">CARD</domain>
+                           <domain from=3D"101" to=3D"427" confidence=3D"2=
.1E-123">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+            </clade>
+            <clade>
+               <branch_length>0.13172</branch_length>
+               <confidence type=3D"unknown">45.0</confidence>
+               <clade>
+                  <branch_length>0.24915</branch_length>
+                  <confidence type=3D"unknown">95.0</confidence>
+                  <clade>
+                     <branch_length>0.76898</branch_length>
+                     <confidence type=3D"unknown">100.0</confidence>
+                     <clade>
+                        <name>28_DROPS</name>
+                        <branch_length>0.1732</branch_length>
+                        <taxonomy>
+                           <code>DROPS</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"535">
+                              <domain from=3D"112" to=3D"399" confidence=
=3D"1.4E-5">NB-ARC</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                     <clade>
+                        <name>Dark_DROME</name>
+                        <branch_length>0.18863</branch_length>
+                        <taxonomy>
+                           <code>DROME</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length=3D"1421">
+                              <domain from=3D"108" to=3D"397" confidence=
=3D"2.1E-5">NB-ARC</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+                  <clade>
+                     <name>29_AEDAE</name>
+                     <branch_length>0.86398</branch_length>
+                     <taxonomy>
+                        <code>AEDAE</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length=3D"423">
+                           <domain from=3D"109" to=3D"421" confidence=3D"9=
.3E-6">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+               <clade>
+                  <name>30_TRICA</name>
+                  <branch_length>0.97698</branch_length>
+                  <taxonomy>
+                     <code>TRICA</code>
+                  </taxonomy>
+               </clade>
+            </clade>
+         </clade>
+      </clade>
+   </phylogeny>
+</phyloxml>


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 test-data/visualization/phyloviz/4_newick.nhx
--- /dev/null
+++ b/test-data/visualization/phyloviz/4_newick.nhx
@@ -0,0 +1,33 @@
+(((BGIOSIBCA028421_ORYSA:0.423485[&&NHX:S=3DORYSA:O=3DBGIOSIBCA028421.1:G=
=3DBGIOSIBCA028421],
+At5g41150_ARATH:0.273135[&&NHX:S=3DARATH:O=3DAt5g41150.1:G=3DAt5g41150]
+):0.690991[&&NHX:S=3DMagnoliophyta:D=3DN:B=3D100],
+(rad16_SCHPO:0.718598[&&NHX:S=3DSCHPO:O=3DSPCC970.01:G=3DSPCC970.01],
+RAD1_YEAST:1.05456[&&NHX:S=3DYEAST:O=3DYPL022W.1:G=3DYPL022W]
+):0.344838[&&NHX:S=3DAscomycota:D=3DN:B=3D100]
+):0.103849[&&NHX:S=3DEukaryota:D=3DN:B=3D61],
+((((((((ERCC4_HUMAN:0.067531[&&NHX:S=3DHUMAN:O=3DENST00000311895.3:G=3DENS=
G00000175595],
+Ercc4_MOUSE:0.17422[&&NHX:S=3DMOUSE:O=3DENSMUST00000023206.5:G=3DENSMUSG00=
000022545]
+):0.065513[&&NHX:S=3DEuarchontoglires:D=3DN:B=3D100],
+ENSMODT00000006086_MONDO:0.104633[&&NHX:S=3DMONDO:O=3DENSMODT00000006086.2=
:G=3DENSMODG00000004840]
+):0.083764[&&NHX:S=3DTheria:D=3DN:B=3D100],
+Q5ZJP8_CHICK:0.153132[&&NHX:S=3DCHICK:O=3DENSGALT00000004716.2:G=3DENSGALG=
00000002981]
+):0.057998[&&NHX:S=3DAmniota:D=3DN:B=3D100],
+ENSXETT00000024054_XENTR:0.288632[&&NHX:S=3DXENTR:O=3DENSXETT00000024054.2=
:G=3DENSXETG00000010991]
+):0.075713[&&NHX:S=3DTetrapoda:D=3DN:B=3D100],
+(zgc-63468_BRARE:0.2218[&&NHX:S=3DBRARE:O=3DENSDART00000015780.4:G=3DENSDA=
RG00000014161],
+NEWSINFRUT00000137921_FUGRU:0.220441[&&NHX:S=3DFUGRU:O=3DNEWSINFRUT0000013=
7921.3:G=3DNEWSINFRUG00000130312]
+):0.170605[&&NHX:S=3DClupeocephala:D=3DN:B=3D100]
+):0.238713[&&NHX:S=3DEuteleostomi:D=3DN:B=3D100],
+ENSCINT00000011737_CIOIN:0.623567[&&NHX:S=3DCIOIN:O=3DENSCINT00000011737.2=
:G=3DENSCING00000005673]
+):0.07499[&&NHX:S=3DChordata:D=3DN:B=3D100],
+(Sm00.scaff00195.0600_SCHMA:0.784609[&&NHX:S=3DSCHMA:O=3DSm00.scaff00195.0=
600:G=3DSm00.scaff00195.0600],
+(CBG03141_CAEBR:0.093703[&&NHX:S=3DCAEBR:O=3DCBG03141:G=3DCBG03141],
+NP_496498_CAEEL:0.212236[&&NHX:S=3DCAEEL:O=3DC47D12.8.1:G=3DC47D12.8]
+):1.47416[&&NHX:S=3DCaenorhabditis:D=3DN:B=3D94]
+):0.26906[&&NHX:S=3DBilateria:D=3DN:B=3D97]
+):0.071406[&&NHX:S=3DBilateria:D=3DN:B=3D1],
+(mei-9-RA_DROME:0.170289[&&NHX:S=3DDROME:O=3DCG3697-RA.3:G=3DCG3697],
+GA17620-PA_DROPS:0.154817[&&NHX:S=3DDROPS:O=3DGA17620-PA:G=3DGA17620]
+):0.818474[&&NHX:S=3DSophophora:D=3DN:B=3D100]
+):0
+)[&&NHX:S=3DEukaryota:D=3DN];
\ No newline at end of file


diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8=
b02df0ab383366955 test-data/visualization/phyloviz/5_newick.nhx
--- /dev/null
+++ b/test-data/visualization/phyloviz/5_newick.nhx
@@ -0,0 +1,1 @@
+(CAE_ELE_PORCN:0.303421 ,((((DRO_PER_PORCN:0.001000 ,DRO_PSE_PORCN:0.00100=
0 )67:0.141994 ,(DRO_ANA_PORCN:0.111899 ,(DRO_ERE_PORCN:0.030516 ,(DRO_MEL_=
PORCN:0.021127 ,DRO_SEC_PORCN:0.021127 )38:0.030516 )35:0.111899 )18:0.1419=
94 )16:0.162611 ,(DRO_WIL_PORCN:0.152225 ,(DRO_VIR_PORCN:0.085057 ,DRO_MOJ_=
PORCN:0.085057 )24:0.152225 )15:0.162611 )13:0.295081 ,(ANO_GAM_PORCN:0.287=
545 ,((CIO_INT_PORCN:0.100686 ,CIO_SAV_PORCN:0.100686 )19:0.275542 ,((LOA_L=
OA_PORCN:0.036278 ,BRU_MAL_PORCN:0.036278 )29:0.272631 ,(((((DAN_RER_PORCN:=
0.086499 ,((TAK_RUB_PORCN:0.032609 ,TET_NIG_PORCN:0.032609 )32:0.048864 ,(G=
AD_MOR_PORCN:0.039387 ,(ORY_LAT_PORCN:0.031729 ,(GAS_ACU_PORCN:0.021882 ,OR=
E_NIL_PORCN:0.021882 )37:0.031729 )34:0.039387 )28:0.048864 )27:0.086499 )2=
3:0.119618 ,(LAT_CHA_PORCN:0.099348 ,((XEN_LAE_PORCN:0.033333 ,XEN_TRO_PORC=
N:0.033333 )31:0.091250 ,(ANO_CAR_PORCN:0.086538 ,((MON_DOM_PORCN:0.014100 =
,(MAC_EUG_PORCN:0.005423 ,SAR_HAR_PORCN:0.005423 )57:0.014100 )42:0.062862 =
,(ORN_ANA_PORCN:0.057974 ,(GOR_GOR_PORCN:0.033876 ,(FEL_CAT_PORCN:0.022851 =
,(PRO_CAP_PORCN:0.019716 ,(CAV_POR_PORCN:0.018599 ,(ERI_EUR_PORCN:0.015518 =
,((DIP_ORD_PORCN:0.007231 ,(MUS_MUS_PORCN:0.001085 ,(RAT_NOR_PORCN:0.001000=
 ,CRI_GRI_PORCN:0.001000 )69:0.001085 )64:0.007231 )53:0.012954 ,(DAS_NOV_P=
ORCN:0.011362 ,(LOX_AFR_PORCN:0.010575 ,(CAL_JAC_PORCN:0.010332 ,(OCH_PRI_P=
ORCN:0.010063 ,(MIC_MUR_PORCN:0.009123 ,(SUS_SCR_PORCN:0.008880 ,(MYO_LUC_P=
ORCN:0.008460 ,((CAN_FAM_PORCN:0.005423 ,AIL_MEL_PORCN:0.005423 )58:0.00809=
3 ,((PTE_VAM_PORCN:0.006508 ,BOS_TAU_PORCN:0.006508 )55:0.007494 ,((SPE_TRI=
_PORCN:0.003254 ,TUP_BEL_PORCN:0.003254 )61:0.006929 ,((OTO_GAR_PORCN:0.001=
085 ,(ORY_CUN_PORCN:0.001000 ,TUR_TRU_PORCN:0.001000 )68:0.001085 )65:0.005=
965 ,(EQU_CAB_PORCN:0.003688 ,(MAC_MUL_PORCN:0.002711 ,(PAN_TRO_PORCN:0.001=
446 ,(HOM_SAP_PORCN:0.001085 ,(PON_ABE_PORCN:0.001000 ,NOM_LEU_PORCN:0.0010=
00 )70:0.001085 )66:0.001446 )63:0.002711 )62:0.003688 )60:0.005965 )56:0.0=
06929 )54:0.007494 )52:0.008093 )51:0.008460 )50:0.008880 )49:0.009123 )48:=
0.010063 )47:0.010332 )46:0.010575 )45:0.011362 )44:0.012954 )43:0.015518 )=
41:0.018599 )40:0.019716 )39:0.022851 )36:0.033876 )30:0.057974 )26:0.06286=
2 )25:0.086538 )22:0.091250 )21:0.099348 )20:0.119618 )17:0.214465 ,(BRA_FL=
O_PORCN:0.189220 ,SAC_KOW_PORCN:0.189220 )12:0.214465 )11:0.257058 ,(NEM_VE=
C_PORCN:0.246631 ,AMP_QUE_PORCN:0.246631 )9:0.257058 )8:0.266904 ,(TRI_CAS_=
PORCN:0.259494 ,(PED_HUM_PORCN:0.227009 ,(NAS_VIT_PORCN:0.160241 ,(API_MEL_=
PORCN:0.031851 ,(BOM_TER_PORCN:0.004808 ,BOM_IMP_PORCN:0.004808 )59:0.03185=
1 )33:0.160241 )14:0.227009 )10:0.259494 )7:0.266904 )6:0.272631 )5:0.27554=
2 )4:0.287545 )3:0.295081 )2:0.303421 )1:0.0001;

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