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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
GNU General Public License v2.0
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`--polytomy` flag seems to be ignored when iqtree is using cmaple #281

Open corneliusroemer opened 2 months ago

corneliusroemer commented 2 months ago

I've used the --pathogen-force cmaple mode a bit recently and noticed that the --polytomy flag seems to be ignored, not having the expected effect of collapsing near-zero-length branches.

I'm using the bioconda binary, which is based on iqtree v2.3.5 with cmaple enabled.

corneliusroemer commented 2 months ago

It seems that one needs to use --output-multifurcating-tree for cmaple instead of --polytomy (something which is not documented in iqtree help string, see #282)