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>.

pftools 2.3                                         May 2003                                              PFW(1)