Multifurcation option --out-mul-tree doesn't seem to work

[corneliusroemer]

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,