gotree collpase length not working?

[tseemann]

cat foo.nwk
((A:0.1,B:0.1),C:0.1);

 gotree collapse length -l 0.2  < foo.nwk
((A:0.1,B:0.1),C:0.1);

I was expecting to see (A:0,B:0,C:0) ?

[fredericlemoine]

I see. First of all, gotree collapse length removes internal branches that are shorter than a given threshold. For example:

$ echo "((A:0.2,B:0.2):0.1,C:0.2,D:0.2);" | gotree collapse length -l 0.2
(C:0.2,D:0.2,A:0.2,B:0.2);

C --0.2-- +       +--0.2-- A     C --0.2-- +  +--0.2-- A
           \     /                          \/
            -0.1-             =>            /\            
           /     \                D --0.2--+  +--0.2-- B
D --0.2--+        +--0.2-- B     

It currently does not remove branches that are connected to the root for rooted tree (root node having degree > 2), because when the root is a polytomy we tend to consider it as unrooted. It is possible to change this behavior though, but will need testing.

[fredericlemoine]

I added options --rootand -tips to collapse brlength, you can have a look at the command documentation. This pre-release implements it. Let me know if it solves your issue.