.TH PAIR_ALIGN 1 "" "pair_align 1.3.8 [tarball]" ""
.SH NAME
pair_align \- Pairwise alignment
.SH SYNOPSIS
\fBpair_align\fP [\fIOPTIONS\fP] \fB-s\fP \fIIN\fP
.SH DESCRIPTION
The program allows one to align two sequences using dyamic programming alignment algorithms while tweaking various parameters.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Main Options:
.TP
\fB-s\fP, \fB--seq\fP \fIINPUT_FILE\fP
FASTA file with two sequences. Valid filetypes are: \fI.frn\fP, \fI.fna\fP, \fI.ffn\fP, \fI.fasta\fP, \fI.faa\fP, and \fI.fa\fP.
.TP
\fB-a\fP, \fB--alphabet\fP \fISTRING\fP
Sequence alphabet. One of \fIprotein\fP, \fIdna\fP, \fIrna\fP, and \fItext\fP. Default: \fIprotein\fP.
.TP
\fB-m\fP, \fB--method\fP \fISTRING\fP
DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence One of \fInw\fP, \fIgotoh\fP, \fIsw\fP, and \fIlcs\fP. Default: \fIgotoh\fP.
.TP
\fB-o\fP, \fB--outfile\fP \fIOUTPUT_FILE\fP
Output filename. Valid filetypes are: \fI.msf\fP, \fI.frn\fP, \fI.fna\fP, \fI.ffn\fP, \fI.fasta\fP, \fI.faa\fP, and \fI.fa\fP. Default: \fIout.fasta\fP.
.SS Scoring Options:
.TP
\fB-g\fP, \fB--gop\fP \fIINTEGER\fP
Gap open penalty. Default: \fI-11\fP.
.TP
\fB-e\fP, \fB--gex\fP \fIINTEGER\fP
Gap extension penalty. Default: \fI-1\fP.
.TP
\fB-ma\fP, \fB--matrix\fP \fISTRING\fP
Score matrix.
.TP
\fB-ms\fP, \fB--msc\fP \fIINTEGER\fP
Match score. Default: \fI5\fP.
.TP
\fB-mm\fP, \fB--mmsc\fP \fIINTEGER\fP
Mismatch penalty. Default: \fI-4\fP.
.SS Banded Alignment Options:
.TP
\fB-lo\fP, \fB--low\fP \fIINTEGER\fP
Lower diagonal.
.TP
\fB-hi\fP, \fB--high\fP \fIINTEGER\fP
Upper diagonal.
.SS DP Matrix Configuration Options:
.TP
\fB-c\fP, \fB--config\fP \fISTRING\fP
Alignment configuration. One of \fIffff\fP, \fIffft\fP, \fIfftf\fP, \fIfftt\fP, \fIftff\fP, \fIftft\fP, \fIfttf\fP, \fIfttt\fP, \fItfff\fP, \fItfft\fP, \fItftf\fP, \fItftt\fP, \fIttff\fP, \fIttft\fP, \fItttf\fP, and \fItttt\fP.
.SH ALIGNMENT CONFIGURATION
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.