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AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
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[Question] Is there a way to use this with a collection of protein fasta files? #34

Closed jolespin closed 3 years ago

jolespin commented 3 years ago

I have several taxonomic groupings and the ORF calls for each of these.

E.g.; taxon_1.faa taxon_2.faa ... taxon_n.faa

Can I use GToTree w/ these files? I do not have genomes for these as they are not bins/MAGs.

AstrobioMike commented 3 years ago

Hi there :)

Absolutely! You can pass a file holding the file names or paths to the -A argument 👍

jolespin commented 3 years ago

Ah @AstrobioMike you are a legend! Looking forward to saving a lot of time using this instead of my messy code from 2 years ago.

Just to be sure, you run it per fasta file right? Not per directory like checkm.