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

pftools 2.1                                       February 1998                                           PFW(1)