.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH PAIR_ALIGN "1" "September 2014" "pair_align 1.4.1+dfsg" "User Commands"
.SH NAME
pair_align \- Pairwise alignment
.PP
SYNOPSIS
.IP
pair_align [OPTIONS] \fB\-s\fR IN.fa
.PP
DESCRIPTION
.IP
The program allows to align two sequences using dyamic programming
alignment algorithms while tweaking various parameters.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
Main Options:
.HP
\fB\-s\fR, \fB\-\-seq\fR IN.fa
.IP
FASTA file with two sequences. Valid filetypes are: fasta and fa.
.HP
\fB\-a\fR, \fB\-\-alphabet\fR ALPHABET
.IP
Sequence alphabet. One of protein, dna, rna, and text. Default:
protein.
.HP
\fB\-m\fR, \fB\-\-method\fR METHOD
.IP
DP alignment method: Needleman\-Wunsch, Gotoh, Smith\-Waterman,
Longest Common Subsequence One of nw, gotoh, sw, and lcs. Default:
gotoh.
.HP
\fB\-o\fR, \fB\-\-outfile\fR OUT
.IP
Output filename. Valid filetypes are: fa, fasta, and msf. Default:
out.fasta.
.IP
Scoring Options:
.HP
\fB\-g\fR, \fB\-\-gop\fR INT
.IP
Gap open penalty. Default: \fB\-11\fR.
.HP
\fB\-e\fR, \fB\-\-gex\fR INT
.IP
Gap extension penalty. Default: \fB\-1\fR.
.HP
\fB\-ma\fR, \fB\-\-matrix\fR MATRIX_FILE
.IP
Score matrix.
.HP
\fB\-ms\fR, \fB\-\-msc\fR INT
.IP
Match score. Default: 5.
.HP
\fB\-mm\fR, \fB\-\-mmsc\fR INT
.IP
Mismatch penalty. Default: \fB\-4\fR.
.IP
Banded Alignment Options:
.HP
\fB\-lo\fR, \fB\-\-low\fR INT
.IP
Lower diagonal.
.HP
\fB\-hi\fR, \fB\-\-high\fR INT
.IP
Upper diagonal.
.IP
DP Matrix Configuration Options:
.HP
\fB\-c\fR, \fB\-\-config\fR CONF
.IP
Alignment configuration. One of ffff, ffft, fftf, fftt, ftff, ftft,
fttf, fttt, tfff, tfft, tftf, tftt, ttff, ttft, tttf, and tttt.
.PP
ALIGNMENT CONFIGURATION
.IP
The alignment configuration is a string of four characters, each being
either t or f. All combinations are allowed. The meaning is as follows.
.TP
tfff
First row initialized with 0s.
.TP
ftff
First column initialized with 0s.
.TP
fftf
Search last column for maximum.
.TP
ffft
Search last row for maximum.
.PP
VERSION
.IP
pair_align version: 1.1
Last update November 2012