How to run raxml on alignment files at genome level

[Karthick Babu Sivakumar]

HI.

I have generated 1500 single copy orthologs in amino acid formats between 10 species.

I have individually aligned them using muscle.

how can i run raxml as all these 1500 alignments to infer the species divergence?

Thanks in advance

[Grimm]

Hi,

the RAxML-based tool for that would be ParGenes: https://github.com/BenoitMorel/ParGenes

and the according original literature.

Cheers, and happy coalescing, Guido

[Alexandros Stamatakis]

Exactly, you would use ParGenes to infer individual gene trees and could
then use GeneRax, SpeciesRax, or AleRax for downstream likelihood-based
gene-tree species tree reconciliation.

Alexis

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Karthick Babu Sivakumar]

Thank you for the information. 

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