Hi, I want to compare trees using some standard metrics. However, the metrics give crazy values when they come across polytomies. They give heavy penalties for small differences in the polytomy. The online literature usually advises you to split them randomly or to split them in the order that they appear in the tree, but again, this causes small changes that cause heavy penalties in the metrics.
major edit: After talking with a colleague, the problem can be simplified to collapsing low-confidence ancestor nodes and sorting polytomies. Does anyone have any code to do that in either R or Perl? (or other!?)