David Emms

Don't worry about 2.5.5, I don't think there are any differences there. The protein sequences might be useful though.

Actually, could you send me the corresponding tree from "WorkingDirectory/Trees_ids/" and also the alignment from "WorkingDirectory/Alignments_ids/" instead? Thanks

I can check the internal "Trees_ids/" file but it looks like it might be because the clade (Osativa_Kitaake_HPIv02_proteins_OsKitaake06g201000.1.v3.1:0.0, Osativa_NipponBare_HPIv02_proteins_LOC_Os06g39040.1.MSUv7.0:0.0) doesn't have a support value in the original tree. That means...

Hi Alastair Thanks, they're good suggestions, I'll try implementing them in the new version. From what I remember I think OrthoFinder only checked the first 100 sequences for performance reasons,...

Hi Alistair Thanks for the example files, I've just got back from holiday and so wasn't able to download the files before the link expired. Would you be able to...

Hi Christopher The STRIDE algorithm is used to find the root of the species tree by using gene duplication events. Sometimes there are not enough to exclude all possible alternative...

Hi shiyi-pan The OrthologuesStats_one-to-one.tsv refers to one-to-one **orthologues** whereas the Orthogroups.GeneCount.tsv file is about **orthogroups**. These are different things. If there are duplications within an orthogroup then you can find...

Hi Stefan Thanks for pointing reporting this, we will look into it. All the best David

Hi Thanks for reporting this, it sounds like a problem with setting up the PYTHONPATH correctly, let me look into what's caused it. In the meantime, if you're able to...

Hi Polly No, I don't think that option is supported, sorry. I think you may be able to manually hack it: what you could do is perform a complete run...