.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH TRANSFORMSEQ "1" "November 2022" "transformseq 1.0.0" "User Commands"
.SH NAME
transformseq \- convert multiple sequence alignments from one format to another
.SH SYNOPSIS
.B transformseq
[\fI\,options\/\fR]  \fI\,< sequence_data.fa > sequence_logo.eps\/\fR
.SH DESCRIPTION
.IP
A tool for converting multiple sequence alignments from one format to
.PP
another.
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR \fB\-\-help\fR
show this help message and exit
.IP
Input/Output Options:
.TP
\fB\-f\fR \fB\-\-fin\fR FILENAME
Sequence input file (default: stdin)
.TP
\fB\-\-format\-in\fR FORMAT
Multiple sequence alignment format: (clustal,
fasta, plain, msf, genbank, nbrf, nexus, phylip,
stockholm, intelligenetics, table, array)
.TP
\fB\-o\fR \fB\-\-fout\fR FILENAME
Output file (default: stdout)
.TP
\fB\-F\fR \fB\-\-format\-out\fR FORMAT
Multiple sequence alignment output format:
(clustal, fasta, plain, intelligenetics, table,
array) (Default: fasta)
.IP
Transformations:
.TP
\fB\-\-seg\fR
Mask low complexity regions in protein sequences.
.TP
\fB\-\-subsample\fR FRACTION
Return a random subsample of the sequences.
.TP
\fB\-\-reverse\fR
reverse sequences
.TP
\fB\-\-complement\fR
complement DNA sequences