spoa

Work in progress!! Spoa 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 alighment modes: local (Smith-Waterman), global (Needleman-Wunsh) and semi-global alignment (overlap).

DEPENDENCIES

LINUX

Application uses following software:

1. gcc 4.*

INSTALLATION

LINUX

Makefile is provided in the project root folder. Inside spoa root, run:

make

After running make, an executable named spoa will appear in the current directory.

USAGE

All examples assume that make has been run and that spoa was successfully compiled.

Spoa must be run as following:

./spoa <sequences.fasta> <match> <missmatch> <gap_open> <gap_extend> <algorithm>

Gap open and extend must be negative values. Supported algorithms are: 0 (local), 1 (global) and 2 (semi-global).

To remove spoa executable, run:

make clean