trcyk(1) 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.