Phyllip body incorrect error - what are the exact format requirements that exabayes needs?

[Ivan Koludarov]

Hello, I've been using exabayes a lot in my work for more than 5 years. However, this recurring error with .phy format is still an enigma to me. I mostly use a combination of UniProt proteins and custom genomically-extracted translated sequences, and I am baffled as to why sometimes it works perfectly, and sometimes refuses to work entirely, forcing me to rename every single sequence to some 10 character code - which is a pain to work with later, forcing me then to rename all names in the .nexus file.

I would highly appreciate if somebody can direct me to the exact specifications of the .phy format that always work for exabayes. That would make my work so much easier.

Thank you,

Ivan

[Alexandros Stamatakis]

Dear Ivan,

Can you send me an example MSA file causing this error.

As far as I remember ExaBayes should support the relaxed PHYLIP format
as specified in the standard RAxML manual on page 8:

https://cme.h-its.org/exelixis/resource/download/NewManual.pdf

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
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org