# cluster.split and unifraq
**URL:** https://forum.mothur.org/t/cluster-split-and-unifraq/1145
**Category:** Theory behind mothur
**Created:** [December 4, 2012, 9:55pm UTC](https://forum.mothur.org/t/cluster-split-and-unifraq/1145 "2012-12-04T21:55:48Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Kendra](https://forum.mothur.org/u/Kendra)
#### Post date: [December 4, 2012, 9:55pm UTC](https://forum.mothur.org/t/cluster-split-and-unifraq/1145/1 "2012-12-04T21:55:48Z")
My computers are currently busy so I’m planning future analyses. I’d like to try unifraq of the sequences (al la “mothur \> unifrac.unweighted(tree=final.phylip.tre, name=final.names, group=final.groups, distance=lt, processors=2, random=F, subsample=4419)”) but the only way that I’ve been able to build my sequence distance matrix is using cluster.split (after following the SOP I still have 300k preclustered “uniques”). Is it possible to use clearcut to generate a nj sequence tree on a distance matrix that doesn’t have overlap between phyla?
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### Author:  [@Kendra](https://forum.mothur.org/u/Kendra)
#### Post date: [January 14, 2013, 7:41pm UTC](https://forum.mothur.org/t/cluster-split-and-unifraq/1145/2 "2013-01-14T19:41:54Z")
Ok so I selected representative sequences for each 95% otu and am trying to build a tree with clearcut, (65k seqs). it’s been running 4 days but hasn’t crashed