Arthur Zwaenepoel

If you are using a random sample as in the example, you might have run in an unlucky situation where you have some empty alignment (well it seems like that...)....

Sorry, I haven't used Singularity containers in two years, so I have a look whether I can update this. For sure `dmd` won't work, because the container doesn't include a...

Does the `tsv` output file with the Ks distribution look fine? If so I would guess it's something with the plotting libraries in your python installation or so. You can...

I can't tell what went wrong for you. If I run ``` wgd viz -ks format.SoyC09.CDS.fasta.ks.tsv ``` I get a perfectly fine histogram (`wgd_hist.svg`).

You did not send me the `Sspon.v20190103.cds.fasta.blast.tsv.mcl.ks_anchors.tsv` file. Are you sure the file looks as expected? You might have some issues in your `wgd syn` command leading to a failure...

Thanks a lot for reporting this, I'll try to get a look to have the `wgd` pipeline figure out when this will happen and report a warning or so when...

Thanks Zhen, nice to see someone helping out! Concerning the `cleandata` thing in PAML, see [this reported bug](https://groups.google.com/g/pamlsoftware/c/whZMV6fcfs4/m/vv6fcinxAgAJ). I had changed some output file formats indeed, but I agree it...

Hi, that is strange, so the `.tsv` files for the Ks distribution and anchor pair Ks distribution are non-empty, but the figures are? Do you get a plot when using...

Strange, for me it works in a fresh environment with the latest version of `wgd` installed from scratch, also for the fragment you pasted above. It must have something to...

Yes, this is just the result of a check performed by `wgd` of whether it can run the `FastTree` executable, maybe I should hide that because it is confusing indeed.