Dear Sergei,

A few requests based on trying to identify groupings of sequences and filter them.

1. When generating a nonparametric bootstrap neighbor joining tree, is it possible to annotate the original tree with the bootstrap support?

2. Given a tree, prune it such that no two tips are less than a user-specified distance apart, and output the sequences related to the pruned tree.

3. Given a tree, identify all clades in which each sequence is within a user-specified distance from each other, and output each clade into a separate file.

Best
Simon