problem about running EPA-GUI version

[Ping]

Dear Dr. Stamatakis, 

I recently got some environmental sequences from marine waters and am trying to place these short sequences in a reference tree. Unfortunately, I got a problem: there is nowhere to set bootstrapping under "EPA Single Gene Alignment" when running EPA GUI version. I am attaching the screenshot of Raxml Workbench which was installed in windows system. I also tried install EPA GUI in Mac OS and got the same result. I'll appreciate if you could please point me in the right direction. Thank you very much for your help.

Best,

Ping

[Pierre Barbera]

Dear Ping,

at least in current versions of EPA, there is no Bootstrap option. I believe this may have been a feature that has since been discontinued. Alexis may be able to provide a more detailed answer to this.

Please note that RAxML Workbench has not been updated for some years, and you may consequently be using a very outdated version of RAxML. My advice would be to download the latest version here:

https://github.com/stamatak/standard-RAxML

And reference the manual for detailed usage instructions. Unfortunately this means using the program from the command line. The most basic usage of EPA should look something like

./raxmlHPC -f v -t <path to reference tree> -s <path to query and reference MSA> -n <some name> -m GTRGAMMA -w <where to write output>

Additionally I would recommend the -G option, as it can speed up processing significantly. With it, a percentage of branches can be specified, such that only the most promising placement locations are evaluated in detail. The manual specifies an example value for this option as 0.1.

Let us know if you have any further questions!

Kind regards,
Pierre Barbera

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[Ping]

Dear Pierre, 

Thank you very much for your kindly and helpful reply. I will download the latest version of Raxml and do EPA with it. Thanks again for your help :)

Best regards,

Ping

[Alexandros Stamatakis]

Thanks Pierre,

An just a note on the bootstrapping for EPA: we abandoned this a long
long time ago, since the expected likelihood weigths worked much better,
especially for short reads ...

Alexis

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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