spoa1
Simd partial order alignment tool
Usage
spoa [options ...]
<sequences>
Overview
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:
-4score for mismatching bases
-g, --gap <int>
-
default:
-8gap 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
Releases
Unchanged in 4 releases since Debian 10 (Buster).