David Emms

Hi If recommend using the example dataset to quickly test that you're doing the right thing to remove species and then do the same with your full dataset. Best wishes...

Hi Baoxing It's something I'm going to be working on over the next few months. There's nothing ready yet but I'll post here when there's something available. All the best...

Thanks for the post/reminder. Yes, it's in the latest release.

Hi Yes, it looks like that is the problem. For some reason not a single orthogroup has at least 50% of your species present (3 species in this case). Are...

Can you include the sequences from the non-DE genes from that species? That will allow OrthoFinder to work out the distribution of gene divergences for that species.

Hi That sounds very normal. If you increase the number of species and if you use RNA-seq data it becomes extremely unlikely that you will find many or any orthogroups...

Hi Abegail If you use the "-M msa" option then OrthoFinder will use multiple sequence alignments for gene tree inference and an alignment file will be produced for each orthogroup....

Hi It looks like you're using ISTREE for tree inference, you can have a look at the log file it produced to see what the problem was, it should be...

Hi It is an issue that occurs unpredictably in IQTREE. In the past I haven't recommended IQTREE because it can be hard to get it to run successfully at the...

Can you send me an email at [email protected] and I will see if I can help. The directories are empty because OrthoFinder had to terminate because the IQTREE species tree...