COMPALIGN(1)						      General Commands Manual						      COMPALIGN(1)

NAME

       compalign - compare two multiple alignments

SYNOPSIS

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

DESCRIPTION

       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.

OPTIONS

       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).

SEE ALSO

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

AUTHOR

       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)