Distance computation algorithms

What algorithm(s) are used to compute distance matrices?

I understand the options in the dist.seqs command, but I’d like to know more about the algorithms used.

With DNADIST, for example, I can use different correction models (FK84, JC, etc.). Is there such an option in mothur?

So we don’t currently include support for the models of multiple substitutions like JC, etc. Part of the reason is that those models ignore gaps. The algorithms in mothur either ignore gaps, count a string of gaps as a single insertion/deletion, or count each gap as an insertion/deletion. Whether to ignore gaps or not can clearly have a significant impact on the distances. We’ll add this to the “list” of future features…