Polyphyletic clusters

[appliedmicrobiologyresearch]

Hi there! I was wondering if you can comment on polyphyletic "bin" clusters, where there are clearly quite phylogenetically distant isolates grouped into the same BAPS cluster? What's the best way of interpreting/ explaining this please? Thanks!

[gtonkinhill]

Hi,

I generally view these clusters as representing the 'background' genetic diversity of the population, with more closely related clusters forming subsets of this broader population-level diversity.

Alternatively, if you already have a phylogeny and your primary goal is to partition it using the BAPs model, you can utilise the best_baps_partition function.