pc-compare - Program for scoring alignments according to a reference alignment with respect to sum-of-

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

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

       This program and its manpage are in the public domain.

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

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

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

       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.

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

pc-compare [TEST_ALIGNMENT] [REFERENCE_ALIGNMENT] [BALIBASE_ANNOT_FILE] [-col] [-core] [-caps]
                  [-annotFILENAME]