trcyk - align sequences to a CM under the TrCYK model
trcyk cmfile seqfile
trcyk reads the covariance model (CM) in cmfile and aligns the
sequences in seqfile to that CM using the TrCYK model for incomplete
data.
The output gives the name of each aligned sequence, the score for the
alignment, and the alignment itself. The ’~’ character in the sequence
indicates residues that have been treated as missing data.