tag:treefam.tenderapp.com,2013-02-16:/discussions/questions/70-adding-gene-to-phylogenyTreeFam: Discussion 2018-10-19T08:27:58Ztag:treefam.tenderapp.com,2013-02-16:Comment/368856082015-06-09T09:47:56Z2015-06-09T09:47:56ZAdding gene to phylogeny<div><p>Hi Patrick.</p>
<p>We don't provide a script for adding a gene to a phylogeny.</p>
<p>But that can be easily done with RAxML, you can try something
like this:</p>
<p>#ML: RAxML_bin -f v -m PROTGAMMAWAG -w RAxML_IN_dir/ -s TF.aln
-t TF.newick -n TF -G 0.05 > RAxML_IN_dir/TF.out</p>
<p>#Parsimony: RAxML_EPA_bin -f y -m PROTGAMMAWAG -w
RAxML_Parsimony_IN_dir/ -s TF.aln -t TF.newick -n $TF -G 0.05 >
RAxML_Parsimony_IN_dir/TF.out</p>
<p>Please let us know if you need any further assistance.</p>
<p>Cheers,</p>
<p>Mateus.</p></div>mateustag:treefam.tenderapp.com,2013-02-16:Comment/368856082015-06-09T13:23:16Z2015-06-09T13:23:16ZAdding gene to phylogeny<div><p>Thanks Mateus. Have you had a chance to see my other query? I
can't get the alignment files and newick files for some of the
Treefams...</p>
<hr></div>McGrath, Patrick Ttag:treefam.tenderapp.com,2013-02-16:Comment/368856082015-06-09T13:26:52Z2015-06-09T13:27:20ZAdding gene to phylogeny<div><p>Hi Patrick.</p>
<p>I hope that was useful. Yes, I'm checking it right now. I'll get
back to you asap.</p>
<p>We regained access to the forum, so from now on the queries
should come direct to us.</p>
<p>Cheers,</p>
<p>Mateus.</p></div>mateustag:treefam.tenderapp.com,2013-02-16:Comment/368856082015-06-09T13:35:59Z2015-06-09T13:35:59ZAdding gene to phylogeny<div><p>Very useful yes. THanks for your help.</p>
<hr>
<p>From: mateus <a href="mailto:tender2+d8305ccd15@tenderapp.com">tender2+d8305ccd15@tenderapp.com</a><br>
Sent: Tuesday, June 09, 2015 9:26 AM<br>
To: McGrath, Patrick T<br>
Subject: TreeFam support: Adding gene to phylogeny [Questions]</p>
<p>?</p></div>McGrath, Patrick T