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'.
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