Fast approximate string searching

GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment

Benchmarking pairwise aligners

A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region

Fast pairwise sequence alignment using SeqAn, in Python.

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

Basic types and functions for pairwise alignment.

Rust bindings for bsalign. A SIMD-based C library for fast partial order alignment and pairwise alignment.

This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

Bioinformatics library

SAM Alignment Reconstructor

Generate random sequence pairs to test pairwise aligners

Top Coder Problem

This repository contains a simple implementation of a pairwise alignment algorithm for FASTA files using the Needleman-Wunsch algorithm.

An R script that calculates a similarity matrix for a list of protein sequences with the aid of Bleakley-Yamanishi Normalized Smith-Waterman Similarity Score.

Python implementation for DNA trace reconstruction with marker code, MIT licensed

Applications that compute pairwise alignments of two biological sequences

R wrapper for running offline BLASTp alignments on curated protein sequence pairs. Originally built for personal use, now being developed into a reusable package for broader community use.

Intro to Bioinformatics course contents