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  • 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, 01:03 AM.

  • #2
    Take a look at CD-HIT.

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    • #3
      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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