David Emms

Hi Steven I was just trying to figure out how to update the display properties of the tree (got it now), so for example I wanted to change the colour...

Hi Pierre Thanks for getting back to me on this. Just a question about the algorithm as I'm curious as to how it works. My understanding of a tree with...

Hi Pierre Thanks for your reply. For me this comes about from a very large scale analysis. It's in support of this website: https://shoot.bio & preprint: https://doi.org/10.1101/2021.09.01.458564. I found your...

For the model, is EPA-ng able to read the IQTREE log file to identify the model used? And are there some IQTREE models it doesn't support, I think I might...

Hi Have you confirmed that you can run diamond yourself using the command format given in config.json? also, if you've downloaded orthofinder from github then it will look in orthofinder's...

Hi Ludo Have you try running the command that OrthoFinder is trying to run? Best wishes David

Hi The code is just trying to open that number of files as a test and it's getting an operating system error, so it looks like a limit on your...

Hi Ricardo Thanks, that's really great! I will put together a page on the tutorials site soon so will mention it there. It'd be great to hear from people here...

I would say that in general for an orthology/orthogroup analysis or species tree it isn't necessary. However, if there is a tree that you are particularly interested in then you...

Hi Michael Hope all's good! I think this has been fixed in the latest release of OrthoFinder (>=v2.5.2). MCL is reporting something but in the older version of OrthoFinder it...