marade

I think what you have in mind might better be termed an all-to-all alignment, where every sequence is compared to every other one and an identity / sim value is...

Distance matrices standardly look like this: sample1 sample2 sample3 sample1 0 2.32 3.32 sample2 3.45 0 1.24 sample3 3.33 6.32 0 So you always have zeros (or 1s) on the...

It sounds like you are making good progress. Looking forward to the results.

Thanks, I appreciate the prompt support. Perhaps you could add some sort of debugging capability so that the issue can be isolated? I'm not eager to run something for hours...

The forest files in the repo are not valid gzip files, and are apparently useless placeholders: $ git clone https://github.com/luntergroup/octopus.git Cloning into 'octopus'... remote: Enumerating objects: 48448, done. remote: Counting...

Indeed the data quota error message is what I'm seeing. Is there something wrong with using Zenodo? Or can someone mirror the files somewhere else temporarily?

The docs for piso.bridge say that 'both' and 'neither' are accepted: https://piso.readthedocs.io/en/latest/reference/api/piso.bridge.html Can we get that updated please?

Thanks. I've found piso to be very useful. I wish pandas would adopt these features and others for Intervals.

I added comments #105 as well. Clearly it's still an issue.

sequence.gb is a file downloaded from GenBank today: $ genovi -o genovi/blah -i sequence.gb -s complete [Errno 2] No such file or directory: 'genovi/blah-temp/contig_1-genovi/blah.faa' Error when transforming gbk to faa....