Benchmarking pairwise aligners

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

Fast approximate string searching

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

Fast pairwise sequence alignment using SeqAn, in Python.

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

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.

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

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

SAM Alignment Reconstructor

Generate random sequence pairs to test pairwise aligners

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.

Top Coder Problem

Applications that compute pairwise alignments of two biological sequences

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

Pipeline to make pairwise comparisons of matched fasta sequences.

Intro to Bioinformatics course contents