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Adding gene to phylogeny

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patrick.mcgrath

20 May, 2015 10:47 AM

Are any of the available perl scripts to download able to add a gene to a phylogeny locally?

1. 1 Posted by mateus on 09 Jun, 2015 09:47 AM

   

   Hi Patrick.

   We don't provide a script for adding a gene to a phylogeny.

   But that can be easily done with RAxML, you can try something like this:

   #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

   #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

   Please let us know if you need any further assistance.

   Cheers,

   Mateus.

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2. 2 Posted by McGrath, Patric... on 09 Jun, 2015 01:23 PM

   

   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...

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3. 3 Posted by mateus on 09 Jun, 2015 01:26 PM

   

   Hi Patrick.

   I hope that was useful. Yes, I'm checking it right now. I'll get back to you asap.

   We regained access to the forum, so from now on the queries should come direct to us.

   Cheers,

   Mateus.

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4. mateus closed this discussion on 09 Jun, 2015 01:26 PM.

5. McGrath, Patrick T re-opened this discussion on 09 Jun, 2015 01:35 PM

6. 4 Posted by McGrath, Patric... on 09 Jun, 2015 01:35 PM

   

   Very useful yes. THanks for your help.

   ________________________________
   From: mateus <[email blocked]>
   Sent: Tuesday, June 09, 2015 9:26 AM
   To: McGrath, Patrick T
   Subject: TreeFam support: Adding gene to phylogeny [Questions]

   ?

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7. Matthieu Muffato closed this discussion on 09 Jun, 2015 02:54 PM.