WEIGHT(1)						      General Commands Manual							 WEIGHT(1)

NAME

       weight - calculates sequence weights for an alignment

SYNOPSIS

       weight [-options] <alignment file>

DESCRIPTION

       This manual page documents briefly the weight command.

       weight is a program that calculates weights for a sequence alignment.

OPTIONS

       Available options:

       -b <f> Use BLOSUM weighting scheme at <f> fractional identity.

       -f <f> Filter out seqs w/ fractional ident > <x> [0-1].

       -h     Help; print version and usage info.

       -o <file>
	      Save weight-annotated alignment in <outfile>.

       -p     Use position based weight scheme (Henikoff & Henikoff).

       -s <n> Sample <n> sequences at random into a new alignment.

       -v     Use Voronoi weight scheme (Sibbald & Argos).

       --informat <s>
	      Specify alignment file format <s>.
	      Allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP.

       --quiet
	      Suppress verbose banner.

SEE ALSO

       afetch(1),  alistat(1),	compalign(1),  compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1),
       stranslate(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						 WEIGHT(1)