tag:treefam.tenderapp.com,2013-02-16:/discussions/problems/52-regarding-the-output-fileTreeFam: Discussion 2016-05-04T17:30:58Ztag:treefam.tenderapp.com,2013-02-16:Comment/397829632016-05-04T17:30:57Z2016-05-04T17:30:57ZRegarding the output file.<div><p>Dear Gauri,</p>
<p>The output in your screenshot already tells you the homologies.
Indeed we don't have (yet) a standalone tool to infer the trees and
the orthologies.<br>
If you want to build orthologies for a whole proteome, you'd
currently have to get the existing alignments + trees of all the
families and run tools yourselves. We'd recommend Mafft + RAxML +
some custom parsing of the trees. Unfortunately all our pipelines
require an infrastructure that is still difficult to setup and is
not much tested outside of our own environment, so I think its cost
would outweigh the burden of running things on your own</p>
<p>Matthieu</p></div>Matthieu Muffato