Benchmarking pairwise aligners

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

Fast pairwise sequence alignment using SeqAn, in Python.

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

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

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!

Biosequence analysis library

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

SAM Alignment Reconstructor

Generate random sequence pairs to test pairwise aligners

Applications that compute pairwise alignments of two biological sequences

Pipeline to make pairwise comparisons of matched fasta sequences.

Pairwise alignment algorithm testing page

If protein sequence NR2F6 is very similar between humans and mice, then mice that have SNP rs11856995 might show photic sneeze reflex (PSR) phenotype.

Sequence Alignment Tool

Projects developed under the Bioinformatics college chair during the 2020/2021 school year

Pairwise genome alignment

An R script to measure the potential influence of different parameters that could have affected the speed of pairwise sequence alignment, using the functions of the Biostrings package.