Very diverse pangenome?

[apredeus]

Hello,

I wanted to look at protein presence-absence of a broader group of genomes (several different orders from alpha-proteobacteria). Would you say it's possible with panX, or should I just run OrthoMCL or something like this?

Thank you!

[rneher]

this will require some fiddling with the thresholds for core-genome identity and completeness. We haven't tried that diverse a set, so I can't really give any good guidance. But I'd be curious how it turns out if you try.