How to compare OTU lists

Hi there- I’ve used other software (usearch) to generate OTUs (clusters) of sequences from three of my samples- I would like to compare these OTUs now, and I’m not sure how I can do that. The goal is to make a cluster tree or heat map or some such output that lets me visualize the data, and also if possible use a test to see if they are indeed different in composition from one another. Can I take this data (fasta files of my OTU representative sequences), import it into mothur, and use some of the hypothesis testing or library comparison commands? Is there a way to export a table that lists sequences found among my samples and which ones are common to which samples, so I can generate a heat map? Can I use mothur for any amplicon, so long as they can be aligned? Can a kind person suggest which commands would be most appropriate to use? I’m not much of a bioinformatician and I’m trying to learn, so advice would be appreciated.

EDIT: OK, I see some of my questions have been answered by the wiki (oops) - but I still am hoping I can use my Usearch-generated OTU data and import it into mothur for sample comparison purposes. I am also hoping I can parse the names of the Usearch OTUs (which contain abundance information) so that can be used as well. Is this possible?


Why not cluster them all together in USearch and then create your own shared file?

I’m hoping to use some of the hypothesis testing algorithms in mothur as well.

Is the read.dist command obsolete? I found a possible solution in some of the examples, but it requires use of this command and I get an error message that it’s an invalid command.

EDIT: OK, I seem to have figured it out now- but someone might want to go and add notes to the analysis examples that use the read.dist command. Thanks for writing this program, it’s doing a lot of things I can’t find ways to do otherwise!