NAME

       pfw - weight sequences of a multiple sequence alignment

SYNOPSIS

       pfw       [  -hm ] [ -N shuffles ] [ -R seed ] [ -W weight ] [ -X gap_excision ] [ ms_file
                 | - ] [ parameters ]

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 ('ms_file') must be either in MSF format as generated  by  GCG  programs  or  by
       readseq  (checksums  are  ignored)  or in MSA format as produced by psa2msa(1).  If '-' is
       specified instead of a filename, the multiple sequence alignment is read from the standard
       input.   pfw  writes a new multiple sequence alignment with modified weights in either MSF
       or MSA format to the standard output.

OPTIONS

       ms_file
              Input multiple sequence alignment file.
              This file contains a multiple sequence alignment in either  MSF  (default)  or  MSA
              format.  If  the format is MSA, pfw will include the new weight of each sequence in
              the FASTA header using the xpsa(5)  keyword  weight.   It  will  thus  replace  any
              existing  weight=value  pair  in the header line.  If the filename is replaced by a
              '-', pfw will read the multiple alignment from stdin.

       -h     Display usage help text.

       -m     Input multiple sequence alignment is in MSA format.

       -N shuffles
              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.
              Type: integer
              Default: 100 (10% precision)

       -R seed
              Seed for the random number generator.
              This  must  be  a  negative  integer  (zero  or  positive integers will be reset to
              negative integers).
              Type: integer
              Default: -123456789

       -W weight
              Total weight.
              The initially computed weights will be multiplied by a constant  factor  such  that
              the sum of all weights equals this value.
              Default: 1

       -X gap_excision
              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: 0.5

PARAMETERS

       Note:  for backwards compatibility, release 2.3 of the  pftools  package  will  parse  the
              version 2.2 style parameters, but these are deprecated and the corresponding option
              (refer to the options section) should be used instead.

       N=#    Shuffles per sequence.
              Use option -N instead.

       R=#    Random number seed.
              Use option -R instead.

       W=#    Total weight.
              Use option -W instead.

       X=#    Gap excision threshold.
              Use option -X instead.

EXIT CODE

       On successful completion of its task, pfw will return an exit  code  of  0.  If  an  error
       occurs,  a  diagnostic  message will be output on standard error and the exit code will be
       different from 0. When conflicting options where passed to the program but the task  could
       nevertheless be completed, warnings will be issued on standard error.

REFERENCES

       Sibbald  PR  &  Argos  P.  (1990).  Weighting aligned protein or nucleic acid sequences to
       correct for unequal representation.  J. Mol. Biol.  216:813-818.

SEE ALSO

       psa2msa(1), psa(5), xpsa(5)

AUTHOR

       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <pftools@sib.swiss>.