Provided by: pftools_3+dfsg-2build1_amd64 
NAME
pfw - weight sequences of a multiple sequence alignment
SYNOPSIS
pfw [ msf-file | - ] [N=#] [X=#] [R=#] [W=#]
DESCRIPTION
pfw computes new weights for individual sequences in a multiple sequence alignment using the method of
Sibbald and Argos (1990). The file containing the multiple sequence alignment (msf-file) must be in MSF
format as generated by GCG programs or by readseq (checksums are ignored). If `-' is specified instead
of a real filename, the multiple sequence alignment is read from the standard input. pfw writes a new
msf-file with modified weights to the standard output.
PARAMETERS
N=# Number of shuffles per sequence to be performed. Note that an average relative precision of r
percent is achieved by approximately (100/r)-squared shuffles. Default: N=100 (10% precision).
X=# Gap excision threshold. This is the minimal fraction of non-gap characters a column of the
multiple sequence alignment must contain in order to be considered for weighting. Default: X=0.5.
R=# Seed for the random number generator. This must be an negative integer (zero or positive integers
will be reset to negative integers). Default=-123456789.
W=# Total weight. The initially computed weights will be multiplied by a constant factor such that the
sum of all weights equals this value. Default: W=1.
Sibbald PR & Argos P (1990). Weighting aligned protein or nucleic acid sequences to correct for unequal
representation. J. Mol. Biol. 216:813-818.
AUTHOR
Philipp Bucher
Philipp.Bucher@isrec.unil.ch