Antw.: [raxml] Computing species tree with RaxML

[alexandros...@gmail.com]

I am not sure I understand your question, with that comman you have already computed a ML tree and bootstrap support, so the next step qould be to visualize the tree and have a look at the support values,

Alexia

Gesendet mit meinem HTC

----- Reply message -----
Von: "Sam" <shishir...@gmail.com>
An: <ra...@googlegroups.com>
Betreff: [raxml] Computing species tree with RaxML
Datum: Di., Apr. 14, 2015 09:26

I have >900 ortholog proteins groups of six metazoans. I concatenated the single copy ortholog in concat_alignments.fa and now want to infer a species tree by using this alignment.
What will be the BEST option to compute such tree?

I run the RaxML with the following option
raxmlHPC-PTHREADS-AVX -f a -T 2 -p 12345 -m PROTGAMMAAUTO -x 12345 -# 1000 -s concat_alignments.fa -m PROTGAMMAAUTO -n T20
Please suggest what should I do next? I read the manual but bit confused.

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[Sam]

I assume, for my case Consensus tree derived from all 1000 bootstrap tree will be the best option. How to do that?
Please correct me if I am wrong: I think the command I used gave me the best ML tree no the consensus one

[Alexandros Stamatakis]

On 14.04.2015 12:39, Sam wrote:
> I assume, for my case Consensus tree derived from all 1000 bootstrap
> tree will be the best option. How to do that?

see manual at:

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf

page 26

> Please correct me if I am wrong: I think the command I used gave me the
> best ML tree no the consensus one

it searched for the best ML tree and also generated BS replicates, it
also wrote a file with the BS support values mapped to the branches of
the best-scoring ML tree,

Alexis

>
> On Tuesday, April 14, 2015 at 12:10:35 PM UTC+2, Alexis wrote:
>
> I am not sure I understand your question, with that comman you have
> already computed a ML tree and bootstrap support, so the next step
> qould be to visualize the tree and have a look at the support values,
>
> Alexia
>
> Gesendet mit meinem HTC
>
> ----- Reply message -----
> Von: "Sam" <shishir...@gmail.com <javascript:>>
> An: <ra...@googlegroups.com <javascript:>>
> Betreff: [raxml] Computing species tree with RaxML
> Datum: Di., Apr. 14, 2015 09:26
>
>
> I have >900 ortholog proteins groups of six metazoans. I
> concatenated the single copy ortholog in concat_alignments.fa and
> now want to infer a species tree by using this alignment.
> What will be the BEST option to compute such tree?
>
> I run the RaxML with the following option
> raxmlHPC-PTHREADS-AVX -f a -T 2 -p 12345 -m PROTGAMMAAUTO -x 12345
> -# 1000 -s concat_alignments.fa -m PROTGAMMAAUTO -n T20
> Please suggest what should I do next? I read the manual but bit
> confused.
>
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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org