matsengrp / gctree

GCtree: phylogenetic inference of genotype-collapsed trees
https://matsengrp.github.io/gctree
GNU General Public License v3.0
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Incorrect dnapars outfile parsing #113

Closed willdumm closed 5 months ago

willdumm commented 1 year ago

Description:

The attached outfile isn't parsed correctly by gctree.phylip_parse.parse_outfile('outfile.txt', root='e', abundance_file='abundances.csv'). In particular, some of the returned trees end up with a single node.

Workaround:

It seems that this has something to do with the name of the outgroup sequence, so for now it should be always possible to fix this by renaming the root to something like 'root' or 'naive'.

outfile.txt abundances.csv