visualize bootsratp tree

[Sam]

I want to generate a bootsrap tree with values. Could you please check the attached file and suggest the option to generate a figure. I used concatenated  orthologs groups for six bacteria from same genus to do RaxML calculations.
Thanks

[J.M.P. Alves]

Sam,

If I did not misunderstand what you have done, I would suggest you use the RAxML_bipartitions.T20 file, which contains the best tree found with the number of partitions already drawn as node labels, and open it in TreeGraph2 or Dendroscope or pretty much any other tree-drawing program, I guess. That's what I do to get a tree like the one you describe.

Best,

J

On Tue, Feb 3, 2015 at 11:49 AM, Sam <shishir...@gmail.com> wrote:

I want to generate a bootsrap tree with values. Could you please check the attached file and suggest the option to generate a figure. I used concatenated  orthologs groups for six bacteria from same genus to do RaxML calculations.
Thanks

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Genomics, Molecular Phylogenetics, Bioinformatics

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[Sam]

Dear Alves,

Thanks for your answer. The command I used was
raxmlHPC-PTHREADS-AVX -T 2 -p 12345 -m PROTGAMMAAUTO -x 12345 -# 10000 -s FcC_smatrix.fas -m PROTGAMMAAUTO -n T20

and it generated the attached two files. How can  generate the missing RAxML_bipartitions.T20? Could you please suggest the command and let me know if I did something wrong with calling raxML?

Thanks

[Fidel Botero]

Hello, Sam.

So, the file you attached contains the 10000 bootstrap replicates you asked RAxML to perform. Now you need a tree on which to map the bootstraps.

I guess you should have a file named "RAxML_bestTree...". This is the tree to use. 
Then, you can ask RAxML to map the bootstraps with the option -f b and providing the tree with the option -t and bootstrap file with the option -z. Check the manual for a full command line. This will generate the "RAxML_bipartition..." file that J. Alves mentioned in his previous message.

Cheers,

Fidel

Fidel Botero
Biologiste
Doctorant Université Montpellier 2
Équipe Phylogénie et Évolution Moléculaires
Institut des Sciences de l'Évolution de Montpellier - ISE-M (UMR 5554 UM2-CNRS)
04 67 14 92 00

[William Gearty]

Hi Sam,

If you have the time, I would just suggest running the full bootstrap/best tree analysis using the -f a command.

This will produce a new set of bootstraps, will find the best tree, and then will map the support values on this best tree.

However, if you don't have the time, you can follow Fidel's instructions.

You will still need to run another analysis to get the best tree which you will then map the support values onto with -f b.

Finally, and perhaps another appealing option, you could just build a consensus tree with the bootstraps you already have using the -J command.

Check out the RAxML manual for more details on this.

Good luck,

Will

William Gearty

people.stanford.edu/wgearty

[Sam]

Dear Fidel,

Thanks, but I already have tried thrice to run the program with the command I wrote but it does not produce the file RAxML_bestTree. I am using Ubuntu12.1.
I suspect there is something wrong with the command line as I am not getting this file RAxML_bestTree. I only get the above attached two files by running the program.

CMD

raxmlHPC-PTHREADS-AVX -T 2 -p 12345 -m PROTGAMMAAUTO -x 12345 -# 10000 -s FcC_smatrix.fas -m PROTGAMMAAUTO -n T20

[Sam]

Thanks you all. I added the -f a option. It works now :)

[Alexandros Stamatakis]

just for the record, one could also:

1. compute a consensus tree from the set of bootstrap trees
2. Just do pure ML searches and then use the -f b option to draw support
values from the BS trees onto the best-scoring ML tree

alexis

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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

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