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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Orthofinder alignment file #709

Open MatteoBrunialti opened 2 years ago

MatteoBrunialti commented 2 years ago

Dear Mr. Emms, I am Matteo Brunialti, a student of bachelor degree of bioinformatics in Sapienza University of Rome, I am currently doing a thesis about horizontal gene transfer.

During the development of my tool I have been using OrthoFinder. If it is not too much trouble I wanted to ask you how to find the alignment file OrthoFinder generates, I've been trying to find a solution via the source code without a solution, since I need those files for later analysis.

Thank you for your help and feedback.

Kind regards, Matteo Brunialti.

lalalagartija commented 2 years ago

The alignment is together with the OGs alignments : MultipleSequenceAlignments/SpeciesTreeAlignment.fa

kcastellano13 commented 2 years ago

I have also not been able to find the alignment files and do not have a MultipleSequenceAlignments folder. Do you have to run Orthofinder with the -m MSA flag to get that output? Thanks in advance!