sourCEntral - mobile manpages

pdf

WEIGHT

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 AT genetics DOT wustl DOT edu

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

pdf