DOKK / manpages / debian 12 / spoa / spoa.1.en
SPOA(1) User Commands SPOA(1)

spoa - SIMD partial order alignment tool

spoa [options ...] <sequences>

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).

<sequences>

input file in FASTA/FASTQ format containing sequences

-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

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

June 2018 spoa 1.1.3