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PAIR_ALIGN(1) User Commands PAIR_ALIGN(1)

NAME

pair_align - Pairwise alignment
SYNOPSIS
pair_align [OPTIONS] -s IN.fa
DESCRIPTION
The program allows to align two sequences using dyamic programming alignment algorithms while tweaking various parameters.
-h, --help
Displays this help message.
--version
Display version information
Main Options:
-s, --seq IN.fa
FASTA file with two sequences. Valid filetypes are: fasta and fa.
-a, --alphabet ALPHABET
Sequence alphabet. One of protein, dna, rna, and text. Default: protein.
-m, --method METHOD
DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence One of nw, gotoh, sw, and lcs. Default: gotoh.
-o, --outfile OUT
Output filename. Valid filetypes are: fa, fasta, and msf. Default: out.fasta.
Scoring Options:
-g, --gop INT
Gap open penalty. Default: -11.
-e, --gex INT
Gap extension penalty. Default: -1.
-ma, --matrix MATRIX_FILE
Score matrix.
-ms, --msc INT
Match score. Default: 5.
-mm, --mmsc INT
Mismatch penalty. Default: -4.
Banded Alignment Options:
-lo, --low INT
Lower diagonal.
-hi, --high INT
Upper diagonal.
DP Matrix Configuration Options:
-c, --config CONF
Alignment configuration. One of ffff, ffft, fftf, fftt, ftff, ftft, fttf, fttt, tfff, tfft, tftf, tftt, ttff, ttft, tttf, and tttt.
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.
tfff
First row initialized with 0s.
ftff
First column initialized with 0s.
fftf
Search last column for maximum.
ffft
Search last row for maximum.
VERSION
pair_align version: 1.1 Last update November 2012
September 2014 pair_align 1.4.1+dfsg