How to run raxml on alignment files at genome level

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Karthick Babu Sivakumar

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May 7, 2024, 5:12:58 AMMay 7
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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

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May 7, 2024, 12:18:37 PMMay 7
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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

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May 10, 2024, 4:07:55 AMMay 10
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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

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May 11, 2024, 4:47:39 AMMay 11
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Thank you for the information. 

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