Sequence Analysis

Usage -i nr60 -o nr30 -c 0.3


Options, -l, -d, -s, -S are same to CD-HIT, here are few more psi-cd-hit specific options:

-ce clustering threshold (blast expect), default -1, by default it doesn't use
    expect threshold, but with positive value, the program cluster sequences if
    similarities meet either identity threshold or expect value threshold
-L  coverage of shorter sequence (aligned / full), default 0
-M  coverage of longer sequence (aligned / full), default 0
-R  (1/0) use psi-blast profile? default 0, perform psi-blast / pdb-blast type
-G  (1/0) use global identity? default 1, sequence identity calculated as
    total identical residues of local alignments / length of shorter sequence
-be blast expect cutoff, default 0.000001
-b  filename of list of hosts, to run this program in parallel with ssh calls

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