TRANSFORMSEQ

NAME

transformseq - convert multiple sequence alignments from one format to another

SYNOPSIS

transformseq [options] < sequence_data.fa > sequence_logo.eps

DESCRIPTION

A tool for converting multiple sequence alignments from one format to

another.

OPTIONS

--version

show program’s version number and exit

-h --help

show this help message and exit

Input/Output Options:

-f --fin FILENAME

Sequence input file (default: stdin)

--format-in FORMAT

Multiple sequence alignment format: (clustal, fasta, plain, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array)

-o --fout FILENAME

Output file (default: stdout)

-F --format-out FORMAT

Multiple sequence alignment output format: (clustal, fasta, plain, intelligenetics, table, array) (Default: fasta)

Transformations:

--seg

Mask low complexity regions in protein sequences.

--subsample FRACTION

Return a random subsample of the sequences.

--reverse

reverse sequences

--complement

complement DNA sequences