PC-COMPARE(1)							  Probcons Manual						     PC-COMPARE(1)

NAME

       pc-compare - Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores.

SYNOPSIS

       pc-compare [TEST_ALIGNMENT] [REFERENCE_ALIGNMENT] [BALIBASE_ANNOT_FILE] [-col] [-core] [-caps] [-annot FILENAME]

NOTE

       pc-compare is named compare in the original sources, but has been remamed to avoid collision with other program names.

SEE ALSO

       pc-makegnufile(1), pc-project(1),from the probcons-extra package, and probcons(1) and probcons-RNA(1) from the probcons package.

REFERENCE

       Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence
       Alignment. Genome Research 15: 330-340.

AUTHORS

       Chuong Do <chuongdo@cs.stanford.edu>
	   Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science,
	   Stanford University.

       Charles Plessy <charles-debian-nospam@plessy.org>
	   Wrote this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       This program and its manpage are in the public domain.

pc-compare 1.12 						    2007-04-04							     PC-COMPARE(1)