Man page - spoa(1)

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    Package:  spoa
    apt-get install spoa
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Manual

SPOA

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Optional
AUTHOR

NAME

spoa - SIMD partial order alignment tool

SYNOPSIS

spoa [options ...] <sequences>

DESCRIPTION

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap).

OPTIONS

<sequences>

input file in FASTA/FASTQ format containing sequences

Optional

-m , --match <int>

default: 5 score for matching bases

-x , --mismatch <int>

default: -4 score for mismatching bases

-g , --gap <int>

default: -8 gap penalty (must be negative)

-l , --algorithm <int>

default: 0 alignment mode:

0 - local (Smith-Waterman) 1 - global (Needleman-Wunsch) 2 - semi-global

-r , --result <int>

default: 0 result mode:

0 - consensus 1 - multiple sequence alignment 2 - 0 & 1

--version

prints the version number

-h , --help

prints the usage

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.