cd-hit 3.1.0 beta (tar/gz)

Release notes:

Several new options added or updated for clustering control and output format.

–G, -aL, -AL, -aS, -AS, and -d

    -G  use global sequence identity, default 1
        if set to 0, then use local sequence identity, calculated as :
        number of identical amino acids in alignment
        divided by the length of the alignment
        NOTE!!! don't use -G 0 unless you use alignment coverage controls
        see options -aL, -AL, -aS, -AS
    -d  length of description in .clstr file, default 20
        if set to 0, it takes the fasta defline and stops at first space
    -aL alignment coverage for the longer sequence, default 0.0
        if set to 0.9, the alignment must covers 90% of the sequence
    -AL alignment coverage control for the longer sequence, default 99999999
        if set to 60, and the length of the sequence is 400,
        then the alignment must be >= 340 (400-60) residues
    -aS alignment coverage for the shorter sequence, default 0.0
        if set to 0.9, the alignment must covers 90% of the sequence
    -AS alignment coverage control for the shorter sequence, default 99999999
        if set to 60, and the length of the sequence is 400,
        then the alignment must be >= 340 (400-60) residues

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Changelog: