details: http://www.bx.psu.edu/hg/galaxy/rev/dd6d09de392e changeset: 3765:dd6d09de392e user: Nate Coraor <nate@bx.psu.edu> date: Mon May 10 12:50:09 2010 -0400 description: Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one diffstat: run.sh | 7 + setup.sh | 1 + tool-data/shared/ucsc/builds.txt | 819 -------------------------------- tool-data/shared/ucsc/builds.txt.sample | 153 +++++ 4 files changed, 161 insertions(+), 819 deletions(-) diffs (1006 lines): diff -r 4e5ca6c44804 -r dd6d09de392e run.sh --- a/run.sh Mon May 10 12:42:05 2010 -0400 +++ b/run.sh Mon May 10 12:50:09 2010 -0400 @@ -20,4 +20,11 @@ fi fi fi + +# Temporary: since builds.txt is now removed from source control, create it +# from the sample if necessary +if [ ! -f "tool-data/shared/ucsc/builds.txt" ]; then + cp tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/builds.txt +fi + python ./scripts/paster.py serve universe_wsgi.ini $@ diff -r 4e5ca6c44804 -r dd6d09de392e setup.sh --- a/setup.sh Mon May 10 12:42:05 2010 -0400 +++ b/setup.sh Mon May 10 12:50:09 2010 -0400 @@ -26,6 +26,7 @@ tool-data/sequence_index_base.loc.sample tool-data/sequence_index_color.loc.sample tool-data/twobit.loc.sample +tool-data/shared/ucsc/builds.txt.sample " DIRS=" diff -r 4e5ca6c44804 -r dd6d09de392e tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Mon May 10 12:42:05 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,819 +0,0 @@ -#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -? unspecified (?) -hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) -hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) -hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) -hg17 Human May 2004 (NCBI35/hg17) (hg17) -hg16 Human July 2003 (NCBI34/hg16) (hg16) -hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) -venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) -panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) -panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) -gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) -gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) -ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) -rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) -papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) -calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) -calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) -otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) -micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) -tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) -mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) -homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) -homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) -sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) -mm9 Mouse July 2007 (NCBI37/mm9) (mm9) -mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) -mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) -rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) -rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) -speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) -cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) -oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) -oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) -ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) -eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) -felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) -felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) -ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) -nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) -canFam2 Dog May 2005 (Broad/canFam2) (canFam2) -canFam1 Dog July 2004 (Broad/canFam1) (canFam1) -canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) -equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) -equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) -susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) -pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) -myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) -susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) -turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) -tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) -proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) -oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) -dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) -choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) -bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) -bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) -bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) -macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) -dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) -dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) -echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) -loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) -loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) -loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) -monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) -monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) -monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) -ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) -galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) -galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) -taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) -anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) -xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) -xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) -danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) -danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) -danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) -danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) -tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) -tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) -fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) -fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) -gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) -oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) -oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) -petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) -borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) -canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) -rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) -priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) -nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) -lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) -homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) -homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) -gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) -eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) -euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) -catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) -afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) -braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) -ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) -ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) -cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) -cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) -strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) -strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) -ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) -ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) -aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) -ce6 C. elegans May 2008 (WS190/ce6) (ce6) -ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) -ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) -ce3 C. elegans March 2005 (WS140/ce3) (ce3) -ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) -caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) -caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) -cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) -cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) -cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) -caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) -caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) -caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) -caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) -caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) -priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) -dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) -dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) -dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) -droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) -droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) -droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) -droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) -droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) -droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) -droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) -dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) -dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) -droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) -droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) -droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) -droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) -droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) -droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) -anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) -apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) -apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) -triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) -falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) -sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) -sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) -sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) -phiX phiX174 (phiX) -16079 Mycobacterium sp. JLS (16079) -symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 (symbTher_IAM14863) -16070 Yersinia pseudotuberculosis IP 31758 (16070) -18883 Mycobacterium tuberculosis H37Ra (18883) -nocaJS61 Nocardioides sp. JS614 (nocaJS61) -12521 Clostridium perfringens SM101 (12521) -acidCryp_JF_5 Acidiphilium cryptum JF-5 (acidCryp_JF_5) -lactLact Lactococcus lactis subsp. lactis Il1403 (lactLact) -13082 Bacillus licheniformis ATCC 14580 (13082) -344 Rhizobium leguminosarum bv. viciae 3841 (344) -siliPome_DSS_3 Silicibacter pomeroyi DSS-3 (siliPome_DSS_3) -paraSp_UWE25 Candidatus Protochlamydia amoebophila UWE25 (paraSp_UWE25) -geobKaus_HTA426 Geobacillus kaustophilus HTA426 (geobKaus_HTA426) -rhizEtli_CFN_42 Rhizobium etli CFN 42 (rhizEtli_CFN_42) -13162 Streptococcus thermophilus LMG 18311 (13162) -13163 Streptococcus thermophilus CNRZ1066 (13163) -18817 Methylobacterium radiotolerans JCM 2831 (18817) -28109 Bartonella tribocorum CIP 105476 (28109) -dichNodo_VCS1703A Dichelobacter nodosus VCS1703A (dichNodo_VCS1703A) -12931 Xanthomonas oryzae pv. oryzae KACC10331 (12931) -eschColi_O157H7 Escherichia coli O157:H7 str. Sakai (eschColi_O157H7) -burk383 Burkholderia sp. 383 (burk383) -15759 Psychrobacter sp. PRwf-1 (15759) -15758 Staphylococcus aureus subsp. aureus JH1 (15758) -27835 Microcystis aeruginosa NIES-843 (27835) -campJeju_81_176 Campylobacter jejuni subsp. jejuni 81-176 (campJeju_81_176) -15751 Rhodopseudomonas palustris BisA53 (15751) -15750 Rhodopseudomonas palustris BisB18 (15750) -15757 Staphylococcus aureus subsp. aureus JH9 (15757) -15756 Xanthobacter autotrophicus Py2 (15756) -15755 Rhodobacter sphaeroides ATCC 17025 (15755) -15754 Rhodobacter sphaeroides ATCC 17029 (15754) -13603 Ralstonia eutropha H16 (13603) -shewPutrCN32 Shewanella putrefaciens CN-32 (shewPutrCN32) -aerPer1 Aeropyrum pernix K1 (aerPer1) -18255 Bacillus thuringiensis str. Al Hakam (18255) -acinSp_ADP1 Acinetobacter sp. ADP1 (acinSp_ADP1) -anapMarg_ST_MARIES Anaplasma marginale str. St. Maries (anapMarg_ST_MARIES) -297 Xanthomonas axonopodis pv. citri str. 306 (297) -desuPsyc_LSV54 Desulfotalea psychrophila LSv54 (desuPsyc_LSV54) -17227 Desulfovibrio vulgaris subsp. vulgaris DP4 (17227) -190 Yersinia enterocolitica subsp. enterocolitica 8081 (190) -193 Clostridium botulinum A str. ATCC 3502 (193) -270 Streptococcus pyogenes str. Manfredo (270) -16252 Synechococcus sp. JA-2-3B'a(2-13) (16252) -16251 Synechococcus sp. JA-3-3Ab (16251) -16319 Arcobacter butzleri RM4018 (16319) -276 Listeria monocytogenes EGD-e (276) -277 Streptococcus pneumoniae TIGR4 (277) -13427 Heliobacterium modesticaldum Ice1 (13427) -279 Staphylococcus epidermidis ATCC 12228 (279) -19979 Flavobacterium psychrophilum JIP02/86 (19979) -13548 Prochlorococcus marinus str. AS9601 (13548) -16700 Yersinia pestis Pestoides F (16700) -therTher_HB8 Thermus thermophilus HB8 (therTher_HB8) -28035 Streptococcus pneumoniae Hungary19A-6 (28035) -19575 Bradyrhizobium sp. ORS278 (19575) -18083 Escherichia coli C str. ATCC 8739 (18083) -methStad1 Methanosphaera stadtmanae DSM 3091 (methStad1) -magnMagn_AMB_1 Magnetospirillum magneticum AMB-1 (magnMagn_AMB_1) -13901 Thermoanaerobacter pseudethanolicus ATCC 33223 (13901) -methBurt2 Methanococcoides burtonii DSM 6242 (methBurt2) -13908 Rhodoferax ferrireducens T118 (13908) -13909 Pseudomonas putida F1 (13909) -16400 Haemophilus influenzae PittEE (16400) -16401 Haemophilus influenzae PittGG (16401) -100 Mycoplasma pulmonis UAB CTIP (100) -methMari_C7 Methanococcus maripaludis C7 (methMari_C7) -106 Halobacterium salinarum R1 (106) -geobSulf Geobacter sulfurreducens PCA (geobSulf) -38 Haemophilus ducreyi 35000HP (38) -28247 Synechococcus sp. PCC 7002 (28247) -16791 Coxiella burnetii RSA 331 (16791) -procMari_CCMP1375 Prochlorococcus marinus subsp. marinus str. CCMP1375 (procMari_CCMP1375) -31 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (31) -oenoOeni_PSU_1 Oenococcus oeni PSU-1 (oenoOeni_PSU_1) -16817 Pseudomonas stutzeri A1501 (16817) -wiggBrev Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis (wiggBrev) -10639 Mycoplasma hyopneumoniae 7448 (10639) -10638 Yersinia pestis biovar Microtus str. 91001 (10638) -caldMaqu1 Caldivirga maquilingensis IC-167 (caldMaqu1) -salmEnte_PARATYPI_ATC Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 (salmEnte_PARATYPI_ATC) -onioYell_PHYTOPLASMA Onion yellows phytoplasma OY-M (onioYell_PHYTOPLASMA) -18459 Francisella tularensis subsp. tularensis WY96-3418 (18459) -334 Streptococcus agalactiae NEM316 (334) -mariAqua_VT8 Marinobacter aquaeolei VT8 (mariAqua_VT8) -16719 Fervidobacterium nodosum Rt17-B1 (16719) -330 Streptococcus agalactiae 2603V/R (330) -333 Streptococcus mutans UA159 (333) -9638 Lactobacillus johnsonii NCC 533 (9638) -17729 Anaeromyxobacter sp. Fw109-5 (17729) -shewLoihPV4 Shewanella loihica PV-4 (shewLoihPV4) -candPela_UBIQUE_HTCC1 Candidatus Pelagibacter ubique HTCC1062 (candPela_UBIQUE_HTCC1) -myxoXant_DK_1622 Myxococcus xanthus DK 1622 (myxoXant_DK_1622) -9636 Rickettsia rickettsii str. 'Sheila Smith' (9636) -salmTyph_TY2 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 (salmTyph_TY2) -chloChlo_CAD3 Chlorobium chlorochromatii CaD3 (chloChlo_CAD3) -mesoFlor_L1 Mesoplasma florum L1 (mesoFlor_L1) -28921 Acinetobacter baumannii (28921) -hermArse Herminiimonas arsenicoxydans (hermArse) -methMaze1 Methanosarcina mazei Go1 (methMaze1) -17343 Sphingomonas wittichii RW1 (17343) -99 Mycoplasma pneumoniae M129 (99) -13643 Synechococcus sp. CC9605 (13643) -13642 Synechococcus sp. WH 7803 (13642) -lawsIntr_PHE_MN1_00 Lawsonia intracellularis PHE/MN1-00 (lawsIntr_PHE_MN1_00) -jannCCS1 Jannaschia sp. CCS1 (jannCCS1) -91 Mycobacterium avium subsp. paratuberculosis K-10 (91) -90 Mycobacterium leprae TN (90) -92 Mycobacterium smegmatis str. MC2 155 (92) -95 Tropheryma whipplei str. Twist (95) -13649 Xanthomonas campestris pv. vesicatoria str. 85-10 (13649) -13885 Chlamydia trachomatis A/HAR-13 (13885) -13884 Rickettsia felis URRWXCal2 (13884) -13887 Streptococcus pyogenes MGAS6180 (13887) -13760 Corynebacterium glutamicum ATCC 13032 (13760) -13888 Streptococcus pyogenes MGAS5005 (13888) -ureaUrea Ureaplasma parvum serovar 3 str. ATCC 700970 (ureaUrea) -streCoel Streptomyces coelicolor A3(2) (streCoel) -orieTsut_BORYONG Orientia tsutsugamushi str. Boryong (orieTsut_BORYONG) -polaJS66 Polaromonas sp. JS666 (polaJS66) -rhodRubr_ATCC11170 Rhodospirillum rubrum ATCC 11170 (rhodRubr_ATCC11170) -rhodRHA1 Rhodococcus sp. RHA1 (rhodRHA1) -pireSp Rhodopirellula baltica SH 1 (pireSp) -franTula_TULARENSIS Francisella tularensis subsp. tularensis SCHU S4 (franTula_TULARENSIS) -syneSp_WH8102 Synechococcus sp. WH 8102 (syneSp_WH8102) -19521 Clostridium botulinum A str. Hall (19521) -238 Staphylococcus aureus subsp. aureus COL (238) -15660 Prochlorococcus marinus str. NATL1A (15660) -17823 Xylella fastidiosa M12 (17823) -methPetr_PM1 Methylibium petroleiphilum PM1 (methPetr_PM1) -237 Staphylococcus aureus subsp. aureus NCTC 8325 (237) -thioCrun_XCL_2 Thiomicrospira crunogena XCL-2 (thioCrun_XCL_2) -haloHalo1 Halobacterium sp. NRC-1 (haloHalo1) -16190 Roseiflexus sp. RS-1 (16190) -idioLoih_L2TR Idiomarina loihiensis L2TR (idioLoih_L2TR) -18637 Methylobacterium extorquens PA1 (18637) -sodaGlos_MORSITANS Sodalis glossinidius str. 'morsitans' (sodaGlos_MORSITANS) -18633 Prochlorococcus marinus str. MIT 9215 (18633) -mycoTube_H37RV Mycobacterium tuberculosis H37Rv (mycoTube_H37RV) -polyQLWP Polynucleobacter sp. QLW-P1DMWA-1 (polyQLWP) -peloLute_DSM273 Pelodictyon luteolum DSM 273 (peloLute_DSM273) -burkCeno_AU_1054 Burkholderia cenocepacia AU 1054 (burkCeno_AU_1054) -13942 Streptococcus sanguinis SK36 (13942) -13943 Burkholderia mallei NCTC 10229 (13943) -ente638 Enterobacter sp. 638 (ente638) -13946 Burkholderia mallei NCTC 10247 (13946) -13947 Burkholderia mallei SAVP1 (13947) -16363 Streptococcus pyogenes MGAS9429 (16363) -neorSenn_MIYAYAMA Neorickettsia sennetsu str. Miyayama (neorSenn_MIYAYAMA) -heliAcin_SHEEBA Helicobacter acinonychis str. Sheeba (heliAcin_SHEEBA) -16366 Streptococcus pyogenes MGAS10750 (16366) -16365 Streptococcus pyogenes MGAS2096 (16365) -13473 Nitrobacter hamburgensis X14 (13473) -burkCepa_AMMD Burkholderia ambifaria AMMD (burkCepa_AMMD) -methMari_C5_1 Methanococcus maripaludis C5 (methMari_C5_1) -13478 Aster yellows witches'-broom phytoplasma AYWB (13478) -13370 Actinobacillus succinogenes 130Z (13370) -methBark1 Methanosarcina barkeri str. Fusaro (methBark1) -geobMeta_GS15 Geobacter metallireducens GS-15 (geobMeta_GS15) -eschColi_CFT073 Escherichia coli CFT073 (eschColi_CFT073) -metMar1 Methanococcus maripaludis S2 (metMar1) -enteFaec_V583 Enterococcus faecalis V583 (enteFaec_V583) -17265 Francisella tularensis subsp. holarctica OSU18 (17265) -shigFlex_2A Shigella flexneri 2a str. 301 (shigFlex_2A) -erwiCaro_ATROSEPTICA Pectobacterium atrosepticum SCRI1043 (erwiCaro_ATROSEPTICA) -pseuHalo_TAC125 Pseudoalteromonas haloplanktis TAC125 (pseuHalo_TAC125) -17163 Campylobacter jejuni subsp. doylei 269.97 (17163) -17161 Campylobacter curvus 525.92 (17161) -10690 Mesorhizobium sp. BNC1 (10690) -10694 Ehrlichia canis str. Jake (10694) -10697 Mycoplasma mobile 163K (10697) -25 Bordetella parapertussis 12822 (25) -26 Bordetella pertussis Tohama I (26) -16841 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) (16841) -sulfToko1 Sulfolobus tokodaii str. 7 (sulfToko1) -404 Lactobacillus brevis ATCC 367 (404) -403 Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (403) -13920 Psychrobacter cryohalolentis K5 (13920) -401 Lactococcus lactis subsp. cremoris SK11 (401) -16137 Bradyrhizobium sp. BTAi1 (16137) -uncuMeth_RCI uncultured methanogenic archaeon RC-I (uncuMeth_RCI) -coryEffi_YS_314 Corynebacterium efficiens YS-314 (coryEffi_YS_314) -13485 Parabacteroides distasonis ATCC 8503 (13485) -409 Mycoplasma gallisepticum R (409) -28743 Yersinia pseudotuberculosis YPIII (28743) -19469 Escherichia coli SECEC SMS-3-5 (19469) -psycArct_273_4 Psychrobacter arcticus 273-4 (psycArct_273_4) -propAcne_KPA171202 Propionibacterium acnes KPA171202 (propAcne_KPA171202) -acidJS42 Acidovorax sp. JS42 (acidJS42) -chroSale_DSM3043 Chromohalobacter salexigens DSM 3043 (chroSale_DSM3043) -19065 Clostridium kluyveri DSM 555 (19065) -18801 Staphylococcus aureus subsp. aureus str. Newman (18801) -13151 Shigella sonnei Ss046 (13151) -18965 Sulfurovum sp. NBC37-1 (18965) -18963 Nitratiruptor sp. SB155-2 (18963) -18809 Methylobacterium sp. 4-46 (18809) -tropWhip_TW08_27 Tropheryma whipplei TW08/27 (tropWhip_TW08_27) -28135 Bordetella petrii DSM 12804 (28135) -natrPhar1 Natronomonas pharaonis DSM 2160 (natrPhar1) -370 Chlamydophila felis Fe/C-56 (370) -377 Gluconacetobacter diazotrophicus PAl 5 (377) -rubrXyla_DSM9941 Rubrobacter xylanophilus DSM 9941 (rubrXyla_DSM9941) -15746 Prochlorococcus marinus str. MIT 9301 (15746) -15747 Rhodopseudomonas palustris HaA2 (15747) -18981 Finegoldia magna ATCC 29328 (18981) -franCcI3 Frankia sp. CcI3 (franCcI3) -15749 Rhodopseudomonas palustris BisB5 (15749) -16549 Janthinobacterium sp. Marseille (16549) -89 Mycobacterium bovis AF2122/97 (89) -12716 Citrobacter koseri ATCC BAA-895 (12716) -82 Lactobacillus acidophilus NCFM (82) -81 Clostridium tetani E88 (81) -16095 Mycoplasma agalactiae PG2 (16095) -87 Corynebacterium diphtheriae NCTC 13129 (87) -84 Lactobacillus gasseri ATCC 33323 (84) -85 Listeria monocytogenes str. 4b F2365 (85) -20197 Francisella tularensis subsp. holarctica FTA (20197) -caldSacc_DSM8903 Caldicellulosiruptor saccharolyticus DSM 8903 (caldSacc_DSM8903) -anabVari_ATCC29413 Anabaena variabilis ATCC 29413 (anabVari_ATCC29413) -lactPlan Lactobacillus plantarum WCFS1 (lactPlan) -carbHydr_Z_2901 Carboxydothermus hydrogenoformans Z-2901 (carbHydr_Z_2901) -13617 Prochlorococcus marinus str. MIT 9515 (13617) -10878 Bacillus anthracis str. Sterne (10878) -16067 Yersinia pestis Angola (16067) -16062 Leuconostoc citreum KM20 (16062) -16148 Leptospira borgpetersenii serovar Hardjo-bovis JB197 (16148) -16146 Leptospira borgpetersenii serovar Hardjo-bovis L550 (16146) -vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 (vibrVuln_CMCP6_1) -10877 Bacillus thuringiensis serovar konkukian str. 97-27 (10877) -19517 Clostridium botulinum A str. ATCC 19397 (19517) -nitrWino_NB_255 Nitrobacter winogradskyi Nb-255 (nitrWino_NB_255) -16321 Bifidobacterium adolescentis ATCC 15703 (16321) -17629 Pseudomonas putida GB-1 (17629) -17237 Rickettsia bellii OSU 85-389 (17237) -19519 Clostridium botulinum F str. Langeland (19519) -mesoLoti Mesorhizobium loti MAFF303099 (mesoLoti) -coxiBurn Coxiella burnetii RSA 493 (coxiBurn) -247 Chlamydophila pneumoniae AR39 (247) -acidBact_ELLIN345 Acidobacteria bacterium Ellin345 (acidBact_ELLIN345) -241 Salmonella typhimurium LT2 (241) -16249 Bartonella bacilliformis KC583 (16249) -12997 Acaryochloris marina MBIC11017 (12997) -xyleFast Xylella fastidiosa 9a5c (xyleFast) -13435 Lactobacillus sakei subsp. sakei 23K (13435) -11752 Haemophilus influenzae 86-028NP (11752) -16393 Neisseria meningitidis 053442 (16393) -16394 Thermoanaerobacter sp. X514 (16394) -methKand1 Methanopyrus kandleri AV19 (methKand1) -bifiLong Bifidobacterium longum NCC2705 (bifiLong) -leptInte Leptospira interrogans serovar Lai str. 56601 (leptInte) -burkCeno_HI2424 Burkholderia cenocepacia HI2424 (burkCeno_HI2424) -16364 Streptococcus pyogenes MGAS10270 (16364) -13875 Candidatus Blochmannia pennsylvanicus str. BPEN (13875) -buchSp Buchnera aphidicola str. APS (Acyrthosiphon pisum) (buchSp) -178 Burkholderia pseudomallei K96243 (178) -176 Mycoplasma penetrans HF-2 (176) -pyroCali1 Pyrobaculum calidifontis JCM 11548 (pyroCali1) -chloTepi_TLS Chlorobium tepidum TLS (chloTepi_TLS) -13282 Synechococcus elongatus PCC 6301 (13282) -16800 Pseudomonas entomophila L48 (16800) -picrTorr1 Picrophilus torridus DSM 9790 (picrTorr1) -shewANA3 Shewanella sp. ANA-3 (shewANA3) -13443 Listeria welshimeri serovar 6b str. SLCC5334 (13443) -bdelBact Bdellovibrio bacteriovorus HD100 (bdelBact) -gramFors_KT0803 Gramella forsetii KT0803 (gramFors_KT0803) -184 Clavibacter michiganensis subsp. sepedonicus (184) -189 Streptomyces avermitilis MA-4680 (189) -clavMich_NCPPB_382 Clavibacter michiganensis subsp. michiganensis NCPPB 382 (clavMich_NCPPB_382) -peloCarb Pelobacter carbinolicus DSM 2380 (peloCarb) -20083 Campylobacter hominis ATCC BAA-381 (20083) -saliTrop_CNB_440 Salinispora tropica CNB-440 (saliTrop_CNB_440) -17057 Borrelia afzelii PKo (17057) -campJeju Campylobacter jejuni subsp. jejuni NCTC 11168 (campJeju) -17053 Pseudomonas putida W619 (17053) -12 Pseudomonas fluorescens PfO-1 (12) -15 Xanthomonas campestris pv. campestris str. 8004 (15) -12475 Wolbachia endosymbiont strain TRS of Brugia malayi (12475) -13217 Azoarcus sp. BH72 (13217) -dehaEthe_195 Dehalococcoides ethenogenes 195 (dehaEthe_195) -methTherPT1 Methanosaeta thermophila PT (methTherPT1) -shewMR7 Shewanella sp. MR-7 (shewMR7) -shewMR4 Shewanella sp. MR-4 (shewMR4) -15708 Acidovorax avenae subsp. citrulli AAC00-1 (15708) -19087 Ureaplasma parvum serovar 3 str. ATCC 27815 (19087) -geobUran_RF4 Geobacter uraniireducens Rf4 (geobUran_RF4) -shewDeni Shewanella denitrificans OS217 (shewDeni) -pyrFur2 Pyrococcus furiosus DSM 3638 (pyrFur2) -desuRedu_MI_1 Desulfotomaculum reducens MI-1 (desuRedu_MI_1) -syntFuma_MPOB Syntrophobacter fumaroxidans MPOB (syntFuma_MPOB) -278 Streptococcus pneumoniae R6 (278) -13654 Synechococcus sp. RCC307 (13654) -13655 Synechococcus sp. CC9902 (13655) -16313 Staphylococcus aureus subsp. aureus USA300 (16313) -legiPneu_PHILADELPHIA Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (legiPneu_PHILADELPHIA) -20391 Bacillus pumilus SAFR-032 (20391) -chlaPneu_CWL029 Chlamydophila pneumoniae CWL029 (chlaPneu_CWL029) -16259 Escherichia coli UTI89 (16259) -13067 Bacteroides fragilis YCH46 (13067) -gloeViol Gloeobacter violaceus PCC 7421 (gloeViol) -moorTher_ATCC39073 Moorella thermoacetica ATCC 39073 (moorTher_ATCC39073) -323 Pseudomonas syringae pv. syringae B728a (323) -320 Brucella suis 1330 (320) -roseDeni_OCH_114 Roseobacter denitrificans OCh 114 (roseDeni_OCH_114) -326 Streptococcus agalactiae A909 (326) -327 Pseudomonas fluorescens Pf-5 (327) -325 Ehrlichia chaffeensis str. Arkansas (325) -329 Desulfovibrio desulfuricans G20 (329) -16203 Brucella melitensis biovar Abortus 2308 (16203) -12950 Yersinia pseudotuberculosis IP 32953 (12950) -heliPylo_26695 Helicobacter pylori 26695 (heliPylo_26695) -12952 Rickettsia canadensis str. McKiel (12952) -12953 Rickettsia akari str. Hartford (12953) -16208 Mycoplasma capricolum subsp. capricolum ATCC 27343 (16208) -17375 Francisella tularensis subsp. tularensis FSC198 (17375) -19259 Acholeplasma laidlawii PG-8A (19259) -77 Clostridium acetobutylicum ATCC 824 (77) -74 Bacillus cereus ATCC 10987 (74) -15770 Dehalococcoides sp. BAV1 (15770) -79 Clostridium perfringens str. 13 (79) -78 Clostridium difficile 630 (78) -13624 Bacillus cereus subsp. cytotoxis NVH 391-98 (13624) -13623 Bacillus weihenstephanensis KBAB4 (13623) -tricEryt_IMS101 Trichodesmium erythraeum IMS101 (tricEryt_IMS101) -photLumi Photorhabdus luminescens subsp. laumondii TTO1 (photLumi) -peloTher_SI Pelotomaculum thermopropionicum SI (peloTher_SI) -18789 Shewanella sediminis HAW-EB3 (18789) -therKoda1 Thermococcus kodakarensis KOD1 (therKoda1) -oceaIhey Oceanobacillus iheyensis HTE831 (oceaIhey) -16297 Xanthomonas oryzae pv. oryzae MAFF 311018 (16297) -19639 Methanococcus maripaludis C6 (19639) -blocFlor Candidatus Blochmannia floridanus (blocFlor) -shewW318 Shewanella sp. W3-18-1 (shewW318) -16184 Clostridium phytofermentans ISDg (16184) -17477 Acinetobacter baumannii ATCC 17978 (17477) -therElon Thermosynechococcus elongatus BP-1 (therElon) -13403 Bacillus amyloliquefaciens FZB42 (13403) -17679 Petrotoga mobilis SJ95 (17679) -16374 Streptococcus pneumoniae D39 (16374) -16375 Shigella flexneri 5 str. 8401 (16375) -methBoon1 Candidatus Methanoregula boonei 6A8 (methBoon1) -mariMari_MCS10 Maricaulis maris MCS10 (mariMari_MCS10) -ralsEutr_JMP134 Ralstonia eutropha JMP134 (ralsEutr_JMP134) -baciSubt Bacillus subtilis subsp. subtilis str. 168 (baciSubt) -16372 Buchnera aphidicola str. Cc (Cinara cedri) (16372) -213 Prochlorococcus marinus subsp. pastoris str. CCMP1986 (213) -erytLito_HTCC2594 Erythrobacter litoralis HTCC2594 (erytLito_HTCC2594) -acidCell_11B Acidothermus cellulolyticus 11B (acidCell_11B) -pyrAer1 Pyrobaculum aerophilum str. IM2 (pyrAer1) -xantCamp Xanthomonas campestris pv. campestris str. ATCC 33913 (xantCamp) -thioDeni_ATCC25259 Thiobacillus denitrificans ATCC 25259 (thioDeni_ATCC25259) -28583 Chlamydia trachomatis 434/Bu (28583) -deinRadi Deinococcus radiodurans R1 (deinRadi) -yersPest_CO92 Yersinia pestis CO92 (yersPest_CO92) -28585 Chlamydia trachomatis L2b/UCH-1/proctitis (28585) -wolbEndo_OF_DROSOPHIL Wolbachia endosymbiont of Drosophila melanogaster (wolbEndo_OF_DROSOPHIL) -17153 Streptococcus suis 05ZYH33 (17153) -10689 Kineococcus radiotolerans SRS30216 (10689) -17155 Streptococcus suis 98HAH33 (17155) -17159 Campylobacter concisus 13826 (17159) -ralsSola Ralstonia solanacearum GMI1000 (ralsSola) -10687 Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (10687) -17403 Frankia alni ACN14a (17403) -16871 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 (16871) -12388 Bacillus licheniformis ATCC 14580 (12388) -neisMeni_Z2491_1 Neisseria meningitidis Z2491 (neisMeni_Z2491_1) -saliRube_DSM13855 Salinibacter ruber DSM 13855 (saliRube_DSM13855) -17953 Campylobacter jejuni subsp. jejuni 81116 (17953) -10616 Mycoplasma mycoides subsp. mycoides SC str. PG1 (10616) -13496 Prochlorococcus marinus str. MIT 9303 (13496) -28507 Clostridium botulinum A3 str. Loch Maree (28507) -colwPsyc_34H Colwellia psychrerythraea 34H (colwPsyc_34H) -hyphNept_ATCC15444 Hyphomonas neptunium ATCC 15444 (hyphNept_ATCC15444) -vibrChol1 Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) -deinGeot_DSM11300 Deinococcus geothermalis DSM 11300 (deinGeot_DSM11300) -312 Buchnera aphidicola str. Sg (Schizaphis graminum) (312) -311 Streptococcus pyogenes MGAS315 (311) -metaSedu Metallosphaera sedula DSM 5348 (metaSedu) -314 Clostridium thermocellum ATCC 27405 (314) -lactSali_UCC118 Lactobacillus salivarius UCC118 (lactSali_UCC118) -pediPent_ATCC25745 Pediococcus pentosaceus ATCC 25745 (pediPent_ATCC25745) -flavJohn_UW101 Flavobacterium johnsoniae UW101 (flavJohn_UW101) -mannSucc_MBEL55E Mannheimia succiniciproducens MBEL55E (mannSucc_MBEL55E) -haemSomn_129PT Haemophilus somnus 129PT (haemSomn_129PT) -13145 Shigella dysenteriae Sd197 (13145) -13146 Shigella boydii Sb227 (13146) -17491 Legionella pneumophila str. Corby (17491) -nanEqu1 Nanoarchaeum equitans Kin4-M (nanEqu1) -12508 Staphylococcus haemolyticus JCSC1435 (12508) -13384 Pelobacter propionicus DSM 2379 (13384) -chlaTrac Chlamydia trachomatis D/UW-3/CX (chlaTrac) -haloWals1 Haloquadratum walsbyi DSM 16790 (haloWals1) -13389 Shewanella baltica OS195 (13389) -baciHalo Bacillus halodurans C-125 (baciHalo) -hypeButy1 Hyperthermus butylicus DSM 5456 (hypeButy1) -chroViol Chromobacterium violaceum ATCC 12472 (chroViol) -16088 Francisella tularensis subsp. novicida U112 (16088) -methJann1 Methanocaldococcus jannaschii DSM 2661 (methJann1) -384 Bacillus cereus ATCC 14579 (384) -pastMult Pasteurella multocida subsp. multocida str. Pm70 (pastMult) -386 Pseudomonas aeruginosa UCBPP-PA14 (386) -388 Haemophilus somnus 2336 (388) -16083 Alkaliphilus oremlandii OhILAs (16083) -27853 Francisella philomiragia subsp. philomiragia ATCC 25017 (27853) -16081 Mycobacterium sp. KMS (16081) -cytoHutc_ATCC33406 Cytophaga hutchinsonii ATCC 33406 (cytoHutc_ATCC33406) -nitrEuro Nitrosomonas europaea ATCC 19718 (nitrEuro) -12720 Enterobacter sakazakii ATCC BAA-894 (12720) -therMari Thermotoga maritima MSB8 (therMari) -mycoGeni Mycoplasma genitalium G37 (mycoGeni) -vibrFisc_ES114_1 Vibrio fischeri ES114 (vibrFisc_ES114_1) -pyroIsla1 Pyrobaculum islandicum DSM 4184 (pyroIsla1) -17407 Burkholderia multivorans ATCC 17616 (17407) -13030 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- (13030) -18271 Rickettsia massiliae MTU5 (18271) -21047 Candidatus Desulforudis audaxviator MP104C (21047) -19857 Vibrio harveyi ATCC BAA-1116 (19857) -17639 Parvibaculum lavamentivorans DS-1 (17639) -18059 Mycobacterium bovis BCG str. Pasteur 1173P2 (18059) -vibrPara1 Vibrio parahaemolyticus RIMD 2210633 (vibrPara1) -259 Escherichia coli O157:H7 EDL933 (259) -64 Staphylococcus epidermidis RP62A (64) -neisGono_FA1090_1 Neisseria gonorrhoeae FA 1090 (neisGono_FA1090_1) -66 Streptococcus gordonii str. Challis substr. CH1 (66) -16723 Aeromonas salmonicida subsp. salmonicida A449 (16723) -16230 Mycobacterium ulcerans Agy99 (16230) -16721 Coxiella burnetii Dugway 5J108-111 (16721) -16720 Pseudomonas aeruginosa PA7 (16720) -256 Buchnera aphidicola str. Bp (Baizongia pistaciae) (256) -257 Chlamydophila pneumoniae J138 (257) -novoArom_DSM12444 Novosphingobium aromaticivorans DSM 12444 (novoArom_DSM12444) -15642 Mycobacterium tuberculosis F11 (15642) -azoaSp_EBN1 Azoarcus sp. EbN1 (azoaSp_EBN1) -therTher_HB27 Thermus thermophilus HB27 (therTher_HB27) -metAce1 Methanosarcina acetivorans C2A (metAce1) -glucOxyd_621H Gluconobacter oxydans 621H (glucOxyd_621H) -listInno Listeria innocua Clip11262 (listInno) -sulfAcid1 Sulfolobus acidocaldarius DSM 639 (sulfAcid1) -geobTher_NG80_2 Geobacillus thermodenitrificans NG80-2 (geobTher_NG80_2) -402 Lactobacillus casei ATCC 334 (402) -13960 Escherichia coli E24377A (13960) -13954 Burkholderia pseudomallei 1710b (13954) -17445 Marinomonas sp. MWYL1 (17445) -13967 Corynebacterium jeikeium K411 (13967) -leifXyli_XYLI_CTCB0 Leifsonia xyli subsp. xyli str. CTCB07 (leifXyli_XYLI_CTCB0) -10645 Synechococcus elongatus PCC 7942 (10645) -campFetu_82_40 Campylobacter fetus subsp. fetus 82-40 (campFetu_82_40) -13355 Ehrlichia ruminantium str. Welgevonden (13355) -desuHafn_Y51 Desulfitobacterium hafniense Y51 (desuHafn_Y51) -13356 Ehrlichia ruminantium str. Gardel (13356) -13291 Bacillus clausii KSM-K16 (13291) -16421 Francisella tularensis subsp. holarctica (16421) -therVolc1 Thermoplasma volcanium GSS1 (therVolc1) -soliUsit_ELLIN6076 Solibacter usitatus Ellin6076 (soliUsit_ELLIN6076) -bradJapo Bradyrhizobium japonicum USDA 110 (bradJapo) -methTher1 Methanothermobacter thermautotrophicus str. Delta H (methTher1) -13454 Pseudoalteromonas atlantica T6c (13454) -methAeol1 Methanococcus aeolicus Nankai-3 (methAeol1) -nostSp Nostoc sp. PCC 7120 (nostSp) -sphiAlas_RB2256 Sphingopyxis alaskensis RB2256 (sphiAlas_RB2256) -saccDegr_2_40 Saccharophagus degradans 2-40 (saccDegr_2_40) -408 Shigella flexneri 2a str. 2457T (408) -anaeDeha_2CP_C Anaeromyxobacter dehalogenans 2CP-C (anaeDeha_2CP_C) -bordBron Bordetella bronchiseptica RB50 (bordBron) -rickBell_RML369_C Rickettsia bellii RML369-C (rickBell_RML369_C) -pyroArse1 Pyrobaculum arsenaticum DSM 13514 (pyroArse1) -thioDeni_ATCC33889 Sulfurimonas denitrificans DSM 1251 (thioDeni_ATCC33889) -methSmit1 Methanobrevibacter smithii ATCC 35061 (methSmit1) -halMar1 Haloarcula marismortui ATCC 43049 (halMar1) -9618 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 (9618) -9619 Brucella abortus biovar 1 str. 9-941 (9619) -vermEise_EF01_2 Verminephrobacter eiseniae EF01-2 (vermEise_EF01_2) -granBeth_CGDNIH1 Granulibacter bethesdensis CGDNIH1 (granBeth_CGDNIH1) -alcaBork_SK2 Alcanivorax borkumensis SK2 (alcaBork_SK2) -vibrChol_O395_1 Vibrio cholerae O395 (vibrChol_O395_1) -nitrOcea_ATCC19707 Nitrosococcus oceani ATCC 19707 (nitrOcea_ATCC19707) -campJeju_RM1221 Campylobacter jejuni RM1221 (campJeju_RM1221) -12468 Bacillus cereus E33L (12468) -12469 Streptococcus pyogenes MGAS10394 (12469) -19135 Actinobacillus pleuropneumoniae serovar 3 str. JL03 (19135) -woliSucc Wolinella succinogenes DSM 1740 (woliSucc) -19485 Ochrobactrum anthropi ATCC 49188 (19485) -therPend1 Thermofilum pendens Hrk 5 (therPend1) -19489 Staphylococcus aureus subsp. aureus USA300_TCH1516 (19489) -therFusc_YX Thermobifida fusca YX (therFusc_YX) -12609 Chlorobium phaeobacteroides DSM 266 (12609) -aquiAeol Aquifex aeolicus VF5 (aquiAeol) -heliPylo_J99 Helicobacter pylori J99 (heliPylo_J99) -burkPseu_1106A Burkholderia pseudomallei 1106a (burkPseu_1106A) -azorCaul2 Azorhizobium caulinodans ORS 571 (azorCaul2) -12607 Prosthecochloris vibrioformis DSM 265 (12607) -synePCC6 Synechocystis sp. PCC 6803 (synePCC6) -baumCica_HOMALODISCA Baumannia cicadellinicola str. Hc (Homalodisca coagulata) (baumCica_HOMALODISCA) -355 Chlamydophila abortus S26/3 (355) -28111 Sorangium cellulosum 'So ce 56' (28111) -shewBalt Shewanella baltica OS155 (shewBalt) -therTeng Thermoanaerobacter tengcongensis MB4 (therTeng) -359 Pseudomonas syringae pv. tomato str. DC3000 (359) -19943 Rickettsia rickettsii str. Iowa (19943) -alkaEhrl_MLHE_1 Alkalilimnicola ehrlichei MLHE-1 (alkaEhrl_MLHE_1) -sulSol1 Sulfolobus solfataricus P2 (sulSol1) -15604 Dehalococcoides sp. CBDB1 (15604) -19265 Nitrosopumilus maritimus SCM1 (19265) -19543 Thermotoga sp. RQ2 (19543) -methHung1 Methanospirillum hungatei JF-1 (methHung1) -27803 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 (27803) -28505 Clostridium botulinum B1 str. Okra (28505) -15766 Lactobacillus reuteri F275 (15766) -17929 Burkholderia cenocepacia MC0-3 (17929) -15762 Mycobacterium sp. MCS (15762) -15760 Mycobacterium gilvum PYR-GCK (15760) -15761 Mycobacterium vanbaalenii PYR-1 (15761) -18797 Lactococcus lactis subsp. cremoris MG1363 (18797) -20371 Brucella suis ATCC 23445 (20371) -desuVulg_HILDENBOROUG Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (desuVulg_HILDENBOROUG) -20079 Escherichia coli DH10B (20079) -288 Yersinia pestis KIM (288) -13006 Alkaliphilus metalliredigens QYMF (13006) -13001 Acinetobacter baumannii (13001) -4 Treponema denticola ATCC 35405 (4) -283 Agrobacterium tumefaciens str. C58 (283) -methVann1 Methanococcus vannielii SB (methVann1) -285 Xylella fastidiosa Temecula1 (285) -286 Streptococcus pyogenes MGAS8232 (286) -candCars_RUDDII Candidatus Carsonella ruddii PV (candCars_RUDDII) -336 Anaplasma phagocytophilum HZ (336) -burkMall_ATCC23344 Burkholderia mallei ATCC 23344 (burkMall_ATCC23344) -leucMese_ATCC8293 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 (leucMese_ATCC8293) -burkViet_G4 Burkholderia vietnamiensis G4 (burkViet_G4) -267 Pseudomonas putida KT2440 (267) -266 Staphylococcus aureus subsp. aureus MSSA476 (266) -265 Staphylococcus aureus subsp. aureus MRSA252 (265) -264 Staphylococcus aureus subsp. aureus N315 (264) -17643 Shewanella baltica OS185 (17643) -archFulg1 Archaeoglobus fulgidus DSM 4304 (archFulg1) -13418 Polaromonas naphthalenivorans CJ2 (13418) -18007 Desulfococcus oleovorans Hxd3 (18007) -16304 Sinorhizobium medicae WSM419 (16304) -16306 Caulobacter sp. K31 (16306) -59 Chloroflexus aurantiacus J-10-fl (59) -12530 Synechococcus sp. CC9311 (12530) -13551 Prochlorococcus marinus str. MIT 9211 (13551) -15691 Mycobacterium abscessus (15691) -fusoNucl Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (fusoNucl) -63 Staphylococcus aureus RF122 (63) -heliHepa Helicobacter hepaticus ATCC 51449 (heliHepa) -17249 Thermosipho melanesiensis BI429 (17249) -15596 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (15596) -psycIngr_37 Psychromonas ingrahamii 37 (psycIngr_37) -syntAcid_SB Syntrophus aciditrophicus SB (syntAcid_SB) -salmTyph Salmonella enterica subsp. enterica serovar Typhi str. CT18 (salmTyph) -burkXeno_LB400 Burkholderia xenovorans LB400 (burkXeno_LB400) -trepPall Treponema pallidum subsp. pallidum str. Nichols (trepPall) -neisMeni_MC58_1 Neisseria meningitidis MC58 (neisMeni_MC58_1) -syntWolf_GOETTINGEN Syntrophomonas wolfei subsp. wolfei str. Goettingen (syntWolf_GOETTINGEN) -15644 Thermotoga lettingae TMO (15644) -13913 Nitrosomonas eutropha C91 (13913) -17417 Dinoroseobacter shibae DFL 12 (17417) -13911 Prochlorococcus marinus str. NATL2A (13911) -13910 Prochlorococcus marinus str. MIT 9312 (13910) -250 Ralstonia metallidurans CH34 (250) -13915 Frankia sp. EAN1pec (13915) -13914 Ignicoccus hospitalis KIN4/I (13914) -rhodSpha_2_4_1 Rhodobacter sphaeroides 2.4.1 (rhodSpha_2_4_1) -16235 Escherichia coli 536 (16235) -zymoMobi_ZM4 Zymomonas mobilis subsp. mobilis ZM4 (zymoMobi_ZM4) -rhodPalu_CGA009 Rhodopseudomonas palustris CGA009 (rhodPalu_CGA009) -420 Chlamydophila pneumoniae TW-183 (420) -stapMari1 Staphylothermus marinus F1 (stapMari1) -sinoMeli Sinorhizobium meliloti 1021 (sinoMeli) -bartHens_HOUSTON_1 Bartonella henselae str. Houston-1 (bartHens_HOUSTON_1) -301 Streptococcus pyogenes SSI-1 (301) -19193 Corynebacterium glutamicum R (19193) -304 Clostridium perfringens ATCC 13124 (304) -306 Staphylococcus aureus subsp. aureus MW2 (306) -307 Corynebacterium glutamicum ATCC 13032 (307) -caulCres Caulobacter crescentus CB15 (caulCres) -haheChej_KCTC_2396 Hahella chejuensis KCTC 2396 (haheChej_KCTC_2396) -10784 Bacillus anthracis str. 'Ames Ancestor' (10784) -magnMC1 Magnetococcus sp. MC-1 (magnMC1) -heliPylo_HPAG1 Helicobacter pylori HPAG1 (heliPylo_HPAG1) -pyrHor1 Pyrococcus horikoshii OT3 (pyrHor1) -12514 Brucella ovis ATCC 25840 (12514) -12512 Arthrobacter aurescens TC1 (12512) -actiPleu_L20 Actinobacillus pleuropneumoniae L20 (actiPleu_L20) -paraDeni_PD1222 Paracoccus denitrificans PD1222 (paraDeni_PD1222) -borrBurg Borrelia burgdorferi B31 (borrBurg) -strePyog_M1_GAS Streptococcus pyogenes M1 GAS (strePyog_M1_GAS) -pseuAeru Pseudomonas aeruginosa PAO1 (pseuAeru) -16523 Herpetosiphon aurantiacus ATCC 23779 (16523) -16525 Candidatus Korarchaeum cryptofilum OPF8 (16525) -19619 Lysinibacillus sphaericus C3-41 (19619) -19617 Candidatus Sulcia muelleri GWSS (19617) -saccEryt_NRRL_2338 Saccharopolyspora erythraea NRRL 2338 (saccEryt_NRRL_2338) -methCaps_BATH Methylococcus capsulatus str. Bath (methCaps_BATH) -16645 Yersinia pestis Antiqua (16645) -16646 Yersinia pestis Nepal516 (16646) -12637 Clostridium beijerinckii NCIMB 8052 (12637) -ehrlRumi_WELGEVONDEN Ehrlichia ruminantium str. Welgevonden (ehrlRumi_WELGEVONDEN) -methLabrZ_1 Methanocorpusculum labreanum Z (methLabrZ_1) -vibrVuln_YJ016_1 Vibrio vulnificus YJ016 (vibrVuln_YJ016_1) -13773 Streptococcus thermophilus LMD-9 (13773) -20039 Leptothrix cholodnii SP-6 (20039) -shewAmaz Shewanella amazonensis SB2B (shewAmaz) -13126 Legionella pneumophila str. Lens (13126) -13127 Legionella pneumophila str. Paris (13127) -13120 Mycoplasma hyopneumoniae 232 (13120) -18509 Staphylococcus aureus subsp. aureus Mu3 (18509) -13040 Silicibacter sp. TM1040 (13040) -18267 Candidatus Vesicomyosocius okutanii HA (18267) -methFlag_KT Methylobacillus flagellatus KT (methFlag_KT) -therAcid1 Thermoplasma acidophilum DSM 1728 (therAcid1) -therPetr_RKU_1 Thermotoga petrophila RKU-1 (therPetr_RKU_1) -shewFrig Shewanella frigidimarina NCIMB 400 (shewFrig) -photProf_SS9 Photobacterium profundum SS9 (photProf_SS9) -burkThai_E264 Burkholderia thailandensis E264 (burkThai_E264) -17811 Lactobacillus helveticus DPC 4571 (17811) -229 Chlamydia muridarum Nigg (229) -228 Chlamydophila caviae GPIC (228) -nitrMult_ATCC25196 Nitrosospira multiformis ATCC 25196 (nitrMult_ATCC25196) -223 Mycobacterium tuberculosis CDC1551 (223) -220 Prochlorococcus marinus str. MIT 9313 (220) -20241 Shewanella halifaxensis HAW-EB4 (20241) -20243 Brucella canis ATCC 23365 (20243) -88 Mycobacterium avium 104 (88) -19227 Renibacterium salmoninarum ATCC 33209 (19227) -neisMeni_FAM18_1 Neisseria meningitidis FAM18 (neisMeni_FAM18_1) -arthFB24 Arthrobacter sp. FB24 (arthFB24) -10679 Rickettsia typhi str. Wilmington (10679) -17457 Pseudomonas mendocina ymp (17457) -13959 Escherichia coli HS (13959) -17455 Shewanella woodyi ATCC 51908 (17455) -17109 Salinispora arenicola CNS-205 (17109) -17459 Serratia proteamaculans 568 (17459) -13953 Burkholderia pseudomallei 668 (13953) -10676 Mycoplasma synoviae 53 (10676) -10675 Mycoplasma hyopneumoniae J (10675) -16820 Clostridium novyi NT (16820) -nocaFarc_IFM10152 Nocardia farcinica IFM 10152 (nocaFarc_IFM10152) -13378 Bacteroides vulgatus ATCC 8482 (13378) -16351 Escherichia coli W3110 (16351) -porpGing_W83 Porphyromonas gingivalis W83 (porpGing_W83) -17415 Shewanella pealeana ATCC 700345 (17415) -eschColi_APEC_O1 Escherichia coli APEC O1 (eschColi_APEC_O1) -46 Bacteroides fragilis NCTC 9343 (46) -13462 Roseiflexus castenholzii DSM 13941 (13462) -44 Bartonella quintana str. Toulouse (44) -42 Rickettsia conorii str. Malish 7 (42) -43 Rickettsia prowazekii str. Madrid E (43) -bactThet_VPI_5482 Bacteroides thetaiotaomicron VPI-5482 (bactThet_VPI_5482) -17413 Delftia acidovorans SPH-1 (17413) -haemInfl_KW20 Haemophilus influenzae Rd KW20 (haemInfl_KW20) -brucMeli Brucella melitensis 16M (brucMeli) -haloHalo_SL1 Halorhodospira halophila SL1 (haloHalo_SL1) -pyrAby1 Pyrococcus abyssi GE5 (pyrAby1) -mculMari1 Methanoculleus marisnigri JR1 (mculMari1) -12554 Borrelia garinii PBi (12554) -dechArom_RCB Dechloromonas aromatica RCB (dechArom_RCB) -stapAure_MU50 Staphylococcus aureus subsp. aureus Mu50 (stapAure_MU50) -eschColi_K12 Escherichia coli K12 (eschColi_K12) -12416 Pseudomonas syringae pv. phaseolicola 1448A (12416) -aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) -baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) -shewOnei Shewanella oneidensis MR-1 (shewOnei) -15217 Human herpesvirus 1 (15217) -lMaj5 Leishmania major 2005 (lMaj5) diff -r 4e5ca6c44804 -r dd6d09de392e tool-data/shared/ucsc/builds.txt.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/shared/ucsc/builds.txt.sample Mon May 10 12:50:09 2010 -0400 @@ -0,0 +1,153 @@ +#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn +? unspecified (?) +hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) +hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) +hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) +hg17 Human May 2004 (NCBI35/hg17) (hg17) +hg16 Human July 2003 (NCBI34/hg16) (hg16) +hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) +venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) +panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) +panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) +gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) +gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) +ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) +rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) +papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) +calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) +calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) +otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) +micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) +tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) +mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) +homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) +homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) +sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) +mm9 Mouse July 2007 (NCBI37/mm9) (mm9) +mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) +mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) +rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) +rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) +speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) +cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) +oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) +oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) +ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) +eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) +felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) +felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) +ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) +nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) +canFam2 Dog May 2005 (Broad/canFam2) (canFam2) +canFam1 Dog July 2004 (Broad/canFam1) (canFam1) +canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) +equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) +equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) +susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) +pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) +myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) +susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) +turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) +tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) +proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) +oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) +dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) +choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) +bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) +bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) +bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) +macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) +dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) +dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) +echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) +loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) +loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) +loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) +monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) +monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) +monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) +ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) +galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) +galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) +taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) +anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) +xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) +xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) +danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) +danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) +danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) +danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) +tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) +tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) +fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) +fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) +gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) +oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) +oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) +petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) +borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) +canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) +rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) +priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) +nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) +lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) +homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) +homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) +gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) +eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) +euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) +catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) +afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) +braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) +ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) +ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) +cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) +cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) +strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) +strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) +ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) +ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) +aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) +ce6 C. elegans May 2008 (WS190/ce6) (ce6) +ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) +ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) +ce3 C. elegans March 2005 (WS140/ce3) (ce3) +ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) +caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) +caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) +cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) +cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) +cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) +caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) +caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) +caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) +caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) +caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) +priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) +dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) +dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) +dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) +droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) +droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) +droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) +droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) +droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) +droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) +droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) +dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) +dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) +droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) +droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) +droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) +droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) +droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) +droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) +anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) +apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) +apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) +triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) +falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) +sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) +sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) +sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) +phiX phiX174 (phiX)