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