compalign - compare two multiple alignments

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157
       Email: eddy@genetics.wustl.edu

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
       for the Debian project (but may be used by others).

                                         Mon, 01 Aug 2005 15:28:08 -0300                            COMPALIGN(1)

compalign  calculates the fractional "identity" between the trusted alignment and the test alignment. The
       two files must contain exactly the same sequences, in exactly the same order.

       The identity of the multiple sequence alignments is defined as the averaged identity  over  all  N(N-1)/2
       pairwise alignments.

       The  fractional  identity  of  two sets of pairwise alignments is in turn defined as follows (for aligned
       known sequences k1 and k2, and aligned test sequences t1 and t2):

            matched columns / total columns

            where total columns = the total number of columns in which there is
            a valid (nongap) symbol in k1 or k2;

            matched columns = the number of columns in which one of the
            following is true:

                 k1 and k2 both have valid symbols at a given column; t1 and t2
                 have the same symbols aligned in a column of the t1/t2
                 alignment;

                 k1 has a symbol aligned to a gap in k2; that symbol in t1 is
                 also aligned to a gap;

                 k2 has a symbol aligned to a gap in k1; that symbol in t2 is
                 also aligned to a gap.

       Because scores for all possible pairs are calculated, the algorithm is of order (N^2)L for N sequences of
       length L; large sequence sets will take a while.

       compalign - compare two multiple alignments

       Available options:

       -h     Print short help and usage info.

       -c     Only compare under marked #=CS consensus structure.

       --informat<s>
              Specify that both alignments are in format <s> (MSF, for instance).

       --quiet
              Suppress verbose header (used in regression testing).

afetch(1),  alistat(1),  compstruct(1),  revcomp(1),  seqsplit(1),  seqstat(1),  sfetch(1),   shuffle(1),
       sindex(1), sreformat(1), stranslate(1), weight(1).

compalign [-options] <trusted-alignment> <test-alignment>