- Manual page

NAME - Randomization of a multiple sequence alignment

Syntax [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.


       --format, -f
              Output format [clustal|fasta]. Default  is  the  format  of  the
              input alignment.

       --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
              is "conservative".

       --n, -n
              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: <test.aln

       Write  "completely"  shuffled version of test.aln in ClustalW format to
       STDOUT: --mode complete --format clustal <test.aln

       Write 100 random alignments to files named randomX.aln --n 100 --mask randomX.aln <test.aln


       Stefan Washietl <>

Stefan Washietl
Last modified: Mon Mar 15 12:54:53 CET 2004