David Emms

Just to add, you can get them from the current source code release: https://github.com/davidemms/OrthoFinder/releases/download/2.5.4/OrthoFinder_source.tar.gz

Hi Botond I had to check the code here to remind myself how it works. Basically, when a duplication is observed, OrthoFinder requires evidence that both child nodes correspond to...

Hi In general RAxML is too heavy-weight for a genome wide analysis like this. However, you can investigate running RAxML yourself on a small alignment in your results directory and...

Do you know if it fails at the MSA or tree inference stage? You can look in the directories Results_Jan20_2/WorkingDirectory/Alignments_ids/ and Tree_ids/, there should be a file for each orthogroup...

Hi The rooted species tree is required in order to be able to root the gene trees and thus infer orthologs. It sounds like what you have done is correct,...

Hi Was there any more output that was produced? It's hard to see what's gone wrong because there's no error message here, just the line of code where *something* happened....

Hi Ed I'm afraid I've not seen an issue like that before. I notice that it is under '/mnt', could it be that the location was unmounted when OrthoFinder was...

Hi Sorry for the delay it getting back to this. I can't think of any way of getting OrthoFinder to use an externally calculated MCL results file--there are too many...

Hi I'm not sure what could be causing this, but I notice that there are some extremely short branch lengths e.g. 5e-09 so it would probably best to rule out...

I'll try and look into this. Could I check what version of OrthoFinder you are using?