Command line for dayhoff recoding

[Monique Aouad]

Hello everyone,

I searched online for a simple command line to do recoding of my datasets (Dayhoff 4 and 6 categories) and the tree reconstruction with RaxML but couldn't find any clear answer.

Can anyone give me a simple command line to do this?

Thanks in advance!

[Akifumi Tanabe]

Hello, Monique

I made a Perl script for such purpose. You can get this script from
the following.
https://github.com/astanabe/Phylogears/blob/master/pgrecodeseq.pl

If you have installed Perl execution environment, you can apply
Dayhoff 6-categories recoding to your data by the following command.

perl pgrecodeseq.pl --type=ANY
"ARNDCQEGHILKMFPSTWYVX-01223220144145000554?" inputfile outputfile

Then, apply MULTIGAMMA model to your data.

Best wishes,

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[Alexandros Stamatakis]

Thank you very much Akifumi,

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Monique Aouad]

Thank you so much for your help! I will try to use your script.

Best,

Monique