David Emms

I think the old versions will always be available conda, if you have an old one installed then you may have to force it to update (this is a guess)...

Hi Sorry about that, this issue was fixed previously (60ed2ec8af9027876f3c4c9830fac8d7e089a571) so using the latest version of OrthoFidner should resolve the issue. Best wishes David

Hi There's not any functionality to reduce the number of open files required. Unfortunately, it would require quite a complex re-write of the ortholog inference code and would probably have...

Hi It has failed. You need to provide the complete set of protein sequences for each species you include, it looks like you might have only given it some sequences...

Hi Paschalis In general you are fine skipping orthogroups, but if you do this it is probably best to supply a species tree with the "-s" option, since OrthoFinder might...

I think if you add a line to your Log.txt file like this: ``` WorkingDirectory_Trees: /home/emms/NOBACKUP/ExampleDataset/OrthoFinder/Results_STANDARD/WorkingDirectory/ ``` pointing to the correct WorkingDirectory that might be enough. Have a look at...

Hi This looks nice, could you talk me through this a little more? From what I can see from the script it looks like it takes the 'description' attribute for...

Hi I had a play with the script using Ensembl proteomes but I couldn't get it to work. If it could support those then I think that could increase its...

Putting aside the primary_transcipts.py script for a minute. If I download a few proteomes from Ensembl and run OrthoFinder on them and then the orthogroup_to_gene_name.py script on the results the...

The primary transcripts script is only a minor complication. If the user ran the primary_transcripts.py script their input to OrthoFinder would only contain the gene names (`ENSDARG00000098423.2`) but they would...