debian man page for truncyk_check

trcyk(1)							  Infernal Manual							  trcyk(1)

NAME
       truncyk_check - check alignment under the TrCYK model

SYNOPSIS
       truncyk_check [options] cmfile seqfile

DESCRIPTION
       trcyk  reads  the covariance model (CM) in cmfile and aligns the sequences in seqfile to that CM using the TrCYK model for incomplete data,
       using both the full-memory and divide-and-conquer approaches.  It checks that the scores from both methods match, that the alignments  from
       both methods match, and that the score of each alignment matches the score returned by the program.

       Because	it  does  use  the  full-memory  implementation  of  TrCYK it can be extremely memory intensive; checking only the scores with the
       --scoreonly option or only the divide-and-conquer approach with the --smallonly option is advised for large models and/or long sequences.

OPTIONS
       -h     show help

       --scoreonly
	      Check only the scores, not the alignments (saves memory).

       --smallonly
	      Check only divide-and-conquer, not the full memory implementation (saves memory).

       --stringent
	      Require the two parsetrees to be identical.

Infernal 1.0.2							   October 2009 							  trcyk(1)