calculating unifrac distance between subsets of communities

Integrating mothur with other programs
1

Hello,

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?

Thanks,
Fangqiong

2

You might try the merge.groups command.

pat

3

Thank you! I’ll try!