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In the general options there's this entry:
--out-mul-tree Output the tree in multifurcating format.
However it doesn't seem to have the effect I expect: producing a newick tree that does not have infinitesimally small branches but uses multifurcation instead.
Is this a bug or am I doing something wrong?
This is how I run it:
cmaple \
-aln results/all-clades/masked.fasta \
-st DNA \
--search EXHAUSTIVE \
--out-mul-tree \
--make-consistent \
-nt AUTO \
--overwrite
These are input and output files (remove the txt extension and untar): repro.tar.zst.txt
What seems to happen is that you give 0 branch lengths but don't collapse entirely - maybe this is only an issue in the newick part of the code:
Sample of the newick output, note the 0 - for multifurcation, 0 branches should not exist for internal branches:
5.34403307029e-06,PP_00109ZR:2.70755226666e-05):0,PP_0010A0P:4.33488094131e-05):0,PP_00109JM:1.64588618645e-05):0,PP_00109KK:1.08175527203e-05):0,PP_0010A3H:5.3818221204e-06):0,
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