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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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Support values #5

Open johanneswerner opened 6 years ago

johanneswerner commented 6 years ago

Is it possible to calculate support values in the core genome tree?

Something like this here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810242/

Thank you very much.

rneher commented 6 years ago

The closest thing I can think of is using the support values that RAxML spits out. These are calculated, but we don't currently propagate them through panX though. This would in principle be possible, but newick parsing of support values in Biopython has given us some problem and they aren't handled properly during rerooting. Combined with the fact that I don't think they are very meaningful in recombining bacteria, I have not pushed this direction. But no fundamental limitation...