shuffle-aln.pl - Manual page
shuffle-aln.pl - Randomization of a multiple sequence alignment
shuffle-aln.pl [options] <alignment.aln
A multiple sequence alignment is read from STDIN and a shuffled version
is written to STDOUT. FASTA and ClustalW formats are supported.
Output format [clustal|fasta]. Default is the format of the
--mode Mode of shuffling [conservative|complete]. If set to "conserva-
tive" only columns with the same gap-pattern and conservation
pattern are shuffled. "complete" shuffles all columns. Default
If a integer n>1 is given here, n shuffled versions are written
to files named "sampleX.aln" (see --mask). Default is 1 and out-
put to STDOUT.
--mask Template for output file names. Needs one X which is replaced by
the current sample number. Default is sampleX.aln".
--help, -h, ?
Display help message.
Write a "conservatively" shuffled version of test.aln to STDOUT:
Write "completely" shuffled version of test.aln in ClustalW format to
shuffle-aln.pl --mode complete --format clustal <test.aln
Write 100 random alignments to files named randomX.aln
shuffle-aln.pl --n 100 --mask randomX.aln <test.aln
Stefan Washietl <firstname.lastname@example.org>
Last modified: Mon Mar 15 12:54:53 CET 2004