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Old 06-22-2018, 02:00 AM   #1
prishlyK
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Default Tool for grouping sequences into clusters with homology within each above threshold

Is there a tool/script/algorithm for grouping sequences into bins so that within each group homology for any two sequences is above (or equal to) a certain threshold value (unless there's only one sequence in a bin)? Some sequences may end up being chimeric, some bins may end up containing a single sequence but only if they don't fit into all other bins. Asked this on biostars, but got no replies.

Last edited by prishlyK; 06-22-2018 at 02:03 AM.
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Old 06-22-2018, 04:02 AM   #2
GenoMax
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Take a look at CD-HIT.
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Old 10-09-2018, 03:12 AM   #3
prishlyK
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Thanks! Sorry for taking so long to reply. Great tool. It doesn't seem to allow filtering by target coverage or choosing a "centroid" sequence in a cluster, though
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