Updates in this release include:
-
Bug fix if query was identical (or near identical with only ambiguous sequences differentiating it) to the outgroup, the resulting polytomy was collapsing to the root node, which didn't have a bootstrap or alrt value. The lineage was being assigned but with incorrect support values of 0,0. This is now fixed and the support for being assigned the base of lineage A is now 100 - (100 - alternative lineage 1) - (100-alternative lineage 2) etc... Which is a more satisfying solution.
-
A new flag (
--write-tree) that optionally writes a tree showing the placement of each query sequence in the guide tree. -
Branches that are now non-zero but very very short are being collapsed, which should overall increase accuracy of calls.