distances between and within groups


We would like to be able to calculate the distances between and within groups, using for instance dist.seqs and a groups file. Is this possible in some way? I haven’t been able to find anything that does this yet.


This is essentially what the amova and homova commands do; however, those commands are meant to be run after running dist.shared and so you’d have much smaller distance matrices than you’d have by pyrosequencing.

Thankyou for letting me know about homova, that one looks like it is what we need. However, I am a bit unsure of how to interpret your reply.

From the example on homova it seems like I could do what I want doing first,

pairwise.seqs, outputting a square matrix and
homova. using a designfile with seqnames followed by group

Am I misunderstanding things here?



Sorry… You could run dist.seqs with output=lt. The input to dist.seqs would have to be all of the sequences, not just the unique ones (see deunique.seqs to do this). Then to homova you would give the distance matrix and your group file would substitute for the design matrix.


Sounds great! Thankyou for solving this for us.