pfw computes new weights for individual sequences in a mul-
tiple 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 gener-
ated by GCG programs or by readseq (checksums are ignored)
or in MSA format as produced by psa2msa(1). If '-' is spec-
ified 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.
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.
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: 100 (10% precision)
Seed for the random number generator.
This must be a negative integer (zero or positive inte-
gers will be reset to negative integers).
The initially computed weights will be multiplied by a
constant factor such that the sum of all weights equals
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.
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.
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.
Sibbald PR & Argos P. (1990). Weightingalignedproteinornucleicacidsequencestocorrectforunequalrepresenta-tion. J. Mol. Biol. 216:813-818.
psa2msa(1), psa(5), xpsa(5)
The pftools package was developped by Philipp Bucher.
Any comments or suggestions should be addressed to