fbaumdicker

@Ha-nn-ah recently did a panX analysis of all reference strains from NCBI. For some reference strains, the collection date format includes not only a day, but also a time. Day...

There is a py3 branch. See also this issue: #27 You could use it and see whether it works on your data.

Hi Ignacio, for pangenomes with high diversity there are a couple of parameters which might improve the clustering: - The default diamond e-value cutoff might be too low to report...

A common problem that can cause an empty core genome is a too diverse set of strains/species. Try the option to use a relaxed soft core to get some genes...

Yes, I am. @not-a-feature and I are incorporating a) mutation models representing gene presence-absence evolution, b) fixed clonal backbone phylogenies (this PR), and c) simulating gene transfer instead of conversion....