# How to compare OTU lists
**URL:** https://forum.mothur.org/t/how-to-compare-otu-lists/1122
**Category:** Commands in mothur
**Created:** [November 13, 2012, 2:55pm UTC](https://forum.mothur.org/t/how-to-compare-otu-lists/1122 "2012-11-13T14:55:13Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@Bentelizabeth](https://forum.mothur.org/u/Bentelizabeth)
#### Post date: [November 13, 2012, 2:55pm UTC](https://forum.mothur.org/t/how-to-compare-otu-lists/1122/1 "2012-11-13T14:55:13Z")
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?
Liz
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [November 13, 2012, 6:06pm UTC](https://forum.mothur.org/t/how-to-compare-otu-lists/1122/2 "2012-11-13T18:06:50Z")
Why not cluster them all together in USearch and then create your own shared file?
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### Author:  [@Bentelizabeth](https://forum.mothur.org/u/Bentelizabeth)
#### Post date: [November 13, 2012, 7:45pm UTC](https://forum.mothur.org/t/how-to-compare-otu-lists/1122/3 "2012-11-13T19:45:36Z")
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!