Does orthofinder allow more than one proteome per species as input ?

Question

[Sara]

Dear all,

Does anybody know if Orthofinder tool allows more than one proteome per species as input ?

Thank you

[dthorbur]

I will tentatively say yes, but it depends on what are your research questions. You can simply concatenate proteome files if there are no name clashes. It may emit a warning about duplicated sequences, but I believe you can just ignore this and move on.

However, phylogenetic inferences among species may be affected by doing this. Otherwise, the only other consequence I can think of is the reference/centroid sequence used to assign orthogroups may change.

An alternative to concatenating files is supplying a proteome for each isolate/strain/etc... that you are using and it will treat it as a different species.

[Sara]

Thanks a lot for your response, I didn't get a notification.

Yes, my aim is to find differences between pathogenic and nonpathogenic bacterial strains. So in this case I think it is ok as it can consider them as different species.