Man page - weight(1)

Packages contains this manual

Package:  biosquid
apt-get install biosquid

Manuals in package:
• compstruct(1)
• shuffle(1)
• sreformat(1)
• afetch(1)
• compalign(1)
• alistat(1)
• weight(1)
• seqstat(1)
• sindex(1)
• stranslate(1)
• revcomp(1)
• sfetch(1)
• seqsplit(1)
Documentations in package:
• biosquid

Manual

WEIGHT

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
AUTHOR

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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).

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