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WEIGHT

WEIGHT

Section: User Commands (1) Updated: Mon, 01 Aug 2005 15:28:08 -0300
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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).


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
AUTHOR

This document was created by man2html, using the manual pages.
Time: 21:26:56 GMT, April 16, 2011