bio-alignment

Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences.

Tech

Algorithm is coded in pure C89 without any dependencies.

Installation

bio-alignment requires only C89-compatible compiler and make utility.

$ cd bio-alignment
$ make
$ ./bin/bio-alignment --help
$ ./bin/bio-alignment -i data/in.fasta -o out.fasta -s blosum62 -g -5 -a nw

Tests

The in1.fasta, in2.fasta, in1_1.fasta, in1_2.fasta, in2_1.fasta, in2_1.fasta files, used for testing the utility, are located in the data folder.

The in1.fasta test can be run as follows:

$ ./bin/bio-alignment -i data/in1.fasta

The in1_1.fasta, in1_2.fasta test can be run as follows:

$ ./bin/bio-alignment -i data/in1_1.fasta,data/in1_2.fasta