Alignment file

[abigasin]

Hello,

I was wondering if there was an alignment file for the orthologues hidden within the results folder.

Also, is there a way to add the species name to each header of the orthologues fasta files?

Thank you so much,

Abegail

[davidemms]

Hi Abegail

If you use the "-M msa" option then OrthoFinder will use multiple sequence alignments for gene tree inference and an alignment file will be produced for each orthogroup. If you've already done an analysis then you can extend it with MSAs using "-M msa -fg PREVIOUS_RESULTS_DIRECTORY".

I can't think of a way to add the the species name to each header of the orthogroup fasta files without writing a short script that uses the files "WorkingDirectory/SpeciesIDs.txt" & "WorkingDirectory/SequenceIDs.txt" files. I can look at putting species names in my default in a future OrthoFinder update. That would be in a month or two's time.

Best wishes David

[sara-torre]

Hi David, I would need to add the species names to the headers of the orthogroups fasta file. Have you already created a script for this? Thank you, Sara