Provided by: biosquid_1.9g+cvs20050121-10_amd64 bug


       compalign - compare two multiple alignments


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


       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

       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

                 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.


       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).

              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).


       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

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

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