calculating unifrac distance between subsets of communities


I’m trying to calculate the unifrac distance between OTUs categorized to different subsets within the same community. For example, I have communities A, B, and C made of OTUs 1, 2, 3, 4, 5,6,7,8,9,10. Now I need to subset the OTUs into groups, say 1-3, 4-6, and 7-10, thus I will have 9 subset communities: A(1-3), A(4-6), A(7-10), B(1-3),B(4-6), B(7-10), C(1-3), C(4-6), C(7-10).

With the input in unifrac.unweighted, seems to me the way to create such subset would be manually editing the count_table file. Yet because the count_table file is formatted as unique sequence in each samples, I’m not sure if (and how) that could be edited based on OTUs…

Any tips?


You might try the merge.groups command.


Thank you! I’ll try!