Fast approximate string searching
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Jun 16, 2026 - Rust
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pairwise-alignment
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GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
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Apr 30, 2025 - C
A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water
smith-waterman needleman-wunsch needle water global-alignment sequence-alignment emboss protein-sequence pairwise-alignment local-alignment nucleotide-sequence
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Feb 27, 2025 - Python
convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region
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May 21, 2024 - Crystal
Fast pairwise sequence alignment using SeqAn, in Python.
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Mar 23, 2019 - C++
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
workflow bioinformatics pipeline genomics nextflow comparative-genomics synteny last pairwise-alignment whole-genome-alignment nf-core dot-plot
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Jun 19, 2026 - Nextflow
Basic types and functions for pairwise alignment.
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Jun 4, 2026 - Rust
Rust bindings for bsalign. A SIMD-based C library for fast partial order alignment and pairwise alignment.
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Jun 16, 2026 - Rust
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
python cython smith-waterman needleman-wunsch python-3-6 alignment protein-sequences numba dna-sequences pairwise pairwise-alignment pypy3 gotoh
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Sep 22, 2021 - Python
Bioinformatics library
bioinformatics clustering smith-waterman needleman-wunsch fasta transcription sequence-alignment pairwise-alignment gc-content multiple-sequence-alignment clustalw hirschberg biosequences phylogenetic-dendrograms hierarchical-cluster-analysis
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Jul 20, 2022 - Python
SAM Alignment Reconstructor
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Jul 26, 2018 - Python
Generate random sequence pairs to test pairwise aligners
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Mar 20, 2025 - Rust
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.
r psa computational-biology smith-waterman protein drug-discovery protein-sequences fasta sequence similarity-score sequence-alignment similarity-matrix dti fasta-sequences pairwise-alignment local-alignment smith-waterman-alignment computer-aided-drug-design biostrings dti-prediction
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Dec 23, 2021 - R
This repository contains a simple implementation of a pairwise alignment algorithm for FASTA files using the Needleman-Wunsch algorithm.
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Jun 20, 2024 - C++
Applications that compute pairwise alignments of two biological sequences
javascript java bioinformatics spring-boot swing reactjs dynamic-programming sequence-alignment pairwise-alignment smith-waterman-alignment
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Feb 4, 2026 - Java
Python implementation for DNA trace reconstruction with marker code, MIT licensed
hidden-markov-model probabilistic-graphical-models pairwise-alignment dna-storage trace-reconstruction
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Jan 8, 2023 - Python
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.
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Sep 9, 2025 - R
𧬠This project implements the Needleman-Wunsch algorithm for global sequence alignment.
python needleman-wunsch python3 dynamic-programming global-alignment pairwise-alignment needleman-wunsch-algorithm needleman-wunsch-alignment
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Dec 14, 2024 - Python
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