Hi John, The current link is: http://wiki.galaxyproject.org/FTPUpload We changed our wiki base and many of the older links do not redirect. I'll let our wiki admin Dave know about this and see what can be done. If this comes up again soon, the base always redirects to "http://galaxyproject.org -> http://wiki.galaxyproject.org", and clicking into "Learn" will likely take to you want to go - the primary hub page for user documentation - including the links in tutorials (plus the wiki side navigation bar with a few different search options). And is true that we do not offer large scale EST to genomic alignment on the public server. Galaxy choices such as BLAST+/Megablast are for use with a local or cloud Galaxy instance. When using a local instance, the tool wrapper can be obtained from the Tool Shed (http://toolshed.g2.bx.psu.edu). A cloud ami would have these tools as part of the package. You can also check the Tool Shed for other options - more are added all the time. Local: http://getgalaxy.org Cloud: http://usegalaxy.org/cloud Hopefully this helps, Jen Galaxy team On 2/2/13 3:17 PM, John Phillips wrote:

1.

To Whom it May Concern:

I am using the Galaxy interface, and according to the tutorial screencast, I should be able to upload my own reference genome. The address given in the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not found page. I was wondering if there is an alternative site that can allow me to do this.

Also, I tried to use the est2genome tool in order to try and align my uploaded sequences. It would only allow me to compare two sequences at a time. Is it possible to align a larger number of sequences at once? I understand there are other programs that allow for this kind of procedure (e.g. Sequencher), but I would like to do this in Galaxy.

Thank you for your time,

-- -John G. Phillips Graduate Research Assistant University of Tulsa 231-233-6914

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