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neherlab / pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration
http://pangenome.de
GNU General Public License v3.0
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Very diverse pangenome? #30

Open apredeus opened 4 years ago

apredeus commented 4 years ago

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 commented 4 years ago

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.