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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with sequence-alignment

A curated list of projects in awesome lists tagged with sequence-alignment .

https://github.com/biopython/biopython

Official git repository for Biopython (originally converted from CVS)

bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment

Last synced: 13 May 2025

https://github.com/lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioinformatics genomics sequence-alignment spliced-alignment

Last synced: 23 Apr 2025

https://github.com/lh3/bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bioinformatics fm-index genomics sequence-alignment

Last synced: 10 Apr 2025

https://github.com/bbuchfink/diamond

Accelerated BLAST compatible local sequence aligner.

sequence-alignment

Last synced: 14 May 2025

https://github.com/biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

bioinformatics genomics java parser-library pdb protein-data-bank protein-modification protein-sequences protein-structure sequence-alignment structural-bioinformatics structure-alignment

Last synced: 17 Dec 2025

https://github.com/martinsos/edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment

Last synced: 10 Apr 2025

https://github.com/Martinsos/edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment

Last synced: 30 Mar 2025

https://github.com/seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

bioinformatics blast cpp-concepts cpp20 fasta fastq fm-index modern samtools seqan sequence-alignment sequence-analysis

Last synced: 15 May 2025

https://github.com/lh3/minigraph

Sequence-to-graph mapper and graph generator

bioinformatics genome-graph genomics pan-genome sequence-alignment

Last synced: 05 Apr 2025

https://github.com/microsoft/bistring

Bidirectionally transformed strings

sequence-alignment string

Last synced: 12 Apr 2025

https://github.com/lh3/miniprot

Align proteins to genomes with splicing and frameshift

bioinformatics sequence-alignment

Last synced: 16 May 2025

https://github.com/wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization

Last synced: 15 May 2025

https://github.com/lh3/ksw2

Global alignment and alignment extension

bioinformatics sequence-alignment

Last synced: 22 Aug 2025

https://github.com/moshi4/pymsaviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

bioinformatics genomics matplotlib msa multiple-sequence-alignment python sequence-alignment sequence-analysis visualization

Last synced: 07 May 2025

https://github.com/lh3/unimap

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

bioinformatics genomics sequence-alignment

Last synced: 07 May 2025

https://github.com/kensho-technologies/sequence_align

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

bioinformatics hirschberg natural-language-processing needleman-wunsch nlp pyo3 python rust sequence-alignment

Last synced: 05 Apr 2025

https://github.com/lh3/miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory

bioinformatics sequence-alignment

Last synced: 18 Jul 2025

https://github.com/martinsos/opal

SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)

alignment avx bioinformatics c-plus-plus database-search sequence-alignment smith-waterman

Last synced: 21 Mar 2025

https://github.com/lh3/bioseq-js

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

bioinformatics sequence-alignment

Last synced: 11 Dec 2025

https://github.com/quim0/wfa-gpu

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

bioinformatics cuda gpu pairwise-alignment sequence-alignment

Last synced: 21 Jun 2025

https://github.com/arshajii/ema

Fast & accurate alignment of barcoded short-reads

bioinformatics sequence-alignment

Last synced: 14 Mar 2025

https://github.com/althonos/pyfamsa

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

bioinformatics cython-library genomics multiple-sequence-alignment python-bindings python-library sequence-alignment

Last synced: 09 Apr 2025

https://github.com/datasnakes/orthoevolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

bash bioinformatics biology biosql blast data-science ftp genetics ncbi orthologs orthologues orthology orthology-inference pbs phylogenetics python qsub sequence-alignment sge shell

Last synced: 15 Apr 2025

https://github.com/benhid/pymsa

Scoring multiple sequence alignments with Python

entropy fasta gaps msa python score sequence-alignment sumofpairs

Last synced: 19 Aug 2025

https://github.com/trishume/seqalign_pathing

Rust implementation of sequence alignment / Levenshtein distance by A* acceleration of the DP algorithm

algorithm dynamic-programming example levenshtein-distance rust sequence-alignment

Last synced: 14 Apr 2025

https://github.com/althonos/pymuscle5

Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.

bioinformatics cython-library genomics multiple-sequence-alignment muscle python-bindings python-library sequence-alignment

Last synced: 24 Oct 2025

https://github.com/ppillot/biomsalign

JavaScript library for Multiple Sequence Alignment

alignment bioinformatics javascript minimizer sequence-alignment

Last synced: 05 May 2025

https://github.com/brentp/spacepile

convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

deep-learning genomics sequence-alignment

Last synced: 29 Oct 2025

https://github.com/iosonofabio/seqanpy

Fast pairwise sequence alignment using SeqAn, in Python.

pairwise-alignment python python-wrapper seqan sequence-alignment swig

Last synced: 13 Apr 2025

https://github.com/lignum-vitae/goombay

Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.

alignment distance gotoh gotoh-algorithm hamming-distance hirschberg jaro jaro-winkler levenshtein-distance longest-common-subsequence longest-common-substring needleman-wunsch python python3 ratcliff-obershelp sequence-alignment shortest-common-supersequence similarity smith-waterman waterman-smith-beyer

Last synced: 14 Dec 2025

https://github.com/mhahsler/rmsa

Interface to Popular Multiple Sequence Alignment Tools - R-package

bioinformatics sequence-alignment

Last synced: 08 Jan 2026

https://github.com/sanojpunchihewa/f5n

Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com

android bioinformatics-pipeline minimap2 mobile-genomics nanopolish portable-genomics samtools sequence-alignment toolkit

Last synced: 13 Oct 2025

https://github.com/althonos/pyopal

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

bioinformatics cython-library cython-wrapper genomics needleman-wunsch python-bindings python-library sequence-alignment simd smith-waterman

Last synced: 07 Sep 2025

https://github.com/lh3/editdist-u85

Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance

bioinformatics sequence-alignment

Last synced: 07 May 2025

https://github.com/gagniuc/visual-sequence-alignment-in-vb6

This highly visual and responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time.

dna dna-sequences gap genetics genomics global heatmap match matrix mismatch proteomics rna score sequence-alignment traceback visualization

Last synced: 04 Mar 2025

https://github.com/gata-bio/affine-gaps

Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment

bioinformatics jit levenshtein-algorithm levenshtein-distance needleman-wunsch protein protein-sequences search sequence-alignment smith-waterman string-search

Last synced: 12 Apr 2025

https://github.com/drostlab/rdiamond

Running DIAMOND2 through R

aligner diamond sequence sequence-alignment

Last synced: 26 Jun 2025

https://github.com/gaojunxuan/chrom_mini_graph

Space-efficient minimizer-based pangenome reference graph and haplotype mapping tool

bioinformatics genomics graph-algorithms pangenome read-mapping sequence-alignment

Last synced: 10 May 2025

https://github.com/gagniuc/simple-sequence-alignment-in-vb6

This highly responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time. The purpose of it is to seeks the optimal alignment between two text sequences.

alignment alignment-algorithm dna-sequences global matrix proteins rna score sequence-alignment text vb6 vb6-application vb6-source

Last synced: 27 Jan 2026

https://github.com/nanxstats/ssw-r

🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD

bioinformatics reticulate sequence-alignment simd smith-waterman

Last synced: 22 Apr 2025

https://github.com/iamazeem/ssic

Sequence Similarity and Identity Calculator (DNA + Protein)

bioinformatics biojava dna-sequences hacktoberfest java protein-sequences sequence-alignment

Last synced: 03 Apr 2025

https://github.com/haddocking/whiscy

Bioinformatic tool to predict structural protein-protein interfaces

bioinformatics protein-protein-interaction protein-structure sequence-alignment utrecht-university

Last synced: 21 Jan 2026

https://github.com/gagniuc/jupiter-bioinformatics-v1

Jupiter Bioinformatics (V1) - To find similarities between two words, a manual comparison is required. For words between 4 and 8 letters, such a task can be performed by any of us without the use of a computer. However, what if the objects of comparison are entire phrases/sequences/files?

bioinformatics dna javascript js local rna score sequence-alignment

Last synced: 12 Apr 2025

https://github.com/robaina/filtersam

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

alignment bioinformatics computational-biology genomics python samtools sequence-alignment

Last synced: 19 Mar 2025

https://github.com/tianyishi2001/sequence-alignment-js

Sequence Alignment Algorithms implemented in Javascript, with a command line application

algorithm bioinformatics biology javascript node science sequence-alignment

Last synced: 21 Mar 2025

https://github.com/d-dawg78/comp561-final-project

McGill University - Computational Biology Methods and Research Project

gene-evolution maximum-parsimony needleman-wunsch phylogenetic-trees sequence-alignment

Last synced: 15 Oct 2025

https://github.com/nsbuitrago/libparasail-sys

Rust bindings for the Parasail C library

bioinformatics ffi-bindings sequence-alignment simd

Last synced: 12 Dec 2025

https://github.com/hdescobarh/pairwasm_alignment

This is an experiment implementing a WebAssembly pairwise sequence alignment module in Rust 🦀.

bioinformatics npm-package sequence-alignment webassembly

Last synced: 23 Jan 2026

https://github.com/educorreia932/fcup-binf

🧬 M:CC 2021/2022 - 1ˢᵗ year/ 2ⁿᵈ semester

bioinformatics biological-sequences fcup-abi sequence-alignment university-course

Last synced: 12 Oct 2025

https://github.com/fperraudeau/gphmm

Generalized Pair Hidden Markov Chain Model (GPHMM)

hmm hmm-model hmm-viterbi-algorithm sequence-alignment sequence-to-sequence

Last synced: 12 Sep 2025

https://github.com/cdcgov/clean-genes

A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.

bioinformatics cdc-influenza-division data-cleaning data-normalisation data-normalization data-science fasta ncird ncird-id sequence-alignment sequence-analysis sequence-annotation

Last synced: 15 Apr 2025

https://github.com/tracywong117/sequence-alignment-py-web

Sequence alignment web app using PyTorch and Flask.

sequence-alignment

Last synced: 06 Oct 2025

https://github.com/tracywong117/sequence-alignment-webapp

Sequence alignment vue web app.

sequence-alignment vue

Last synced: 14 Jul 2025

https://github.com/childsish/align-js

Naive implementation of Smith-Waterman in Javascript

javascript sequence-alignment

Last synced: 01 Mar 2025

https://github.com/sameetasadullah/sequence-allignment-parallel-implementation

A Parallel Implementation of strings Sequence Allignment in C++ using MPI (Especially used in Bio-Informatics)

cpp linux mpi sequence-alignment ubuntu

Last synced: 15 Mar 2025

https://github.com/pprattis/sequence-global-alignment-with-unknown-nucleotides

A Python script that for a parameter k, calculates the universal alignment of 2 sequences, with limitation that the alignment contains at most k unknown nucleotides. Nucleotide sequences are sometimes written in a 5-character alphabet, A, T, G, C, and N where N stands for an undefined nucleotide.

bioinformatics chromosomes computer-science fasta global-alignment nucleotides program python sequence-alignment student

Last synced: 29 Mar 2025

https://github.com/zmactep/triealignments.jl

Julia implementation of "Fast Trie-Based Method for Multiple Pairwise Sequence Alignment" paper.

algorithms bioinformatics julia sequence-alignment

Last synced: 11 Jun 2025

https://github.com/samirelanduk/alignjs

Sequence alignment in JavaScript

bioinformatics sequence-alignment

Last synced: 03 Mar 2025

https://github.com/samstan4/genome-scale-comparison

Implementation of large scale genome comparisons. Utilizes McCreight Suffix tree construction algorithm as well as a modified Pairwise Sequence Alignment algorithm with an Affine Gap Penalty. Implemented in C++.

algorithms datastructures genomics matrix sequence-alignment string string-similarity tree-structure trie-structure

Last synced: 27 Jan 2026

https://github.com/niaid/genome-browsers

This repo contains materials for the Genome Browsers course, taught as part of ACE 2021.

ace bcbb-training genome-analysis genome-browser sequence-alignment

Last synced: 26 Jan 2026

https://github.com/clemsciences/sequence_alignment

Sequence alignment algorithms

alignment sequence-alignment

Last synced: 15 May 2025

https://github.com/tejarshaarigila/bioinformatics-sequence-alignment

Python implementations of the Needleman-Wunsch and Smith-Waterman sequence alignment algorithms.

bioinformatics sequence-alignment

Last synced: 08 Apr 2025

https://github.com/andrewdavidsmith/adapto-rs

Remove adaptors from short-read bisulfite sequencing data (coded in rust)

sequence-alignment sequencer sequencing sequencing-adapters sequencing-data sequencing-data-analysis sequencing-reads

Last synced: 26 Mar 2025

https://github.com/chrisarg/bio-seqalignment

Main page of the Bio::SeqAlignment project

bioinformatics sequence-alignment

Last synced: 26 Mar 2025

https://github.com/chrisarg/bio-seqalignment-examples-enhancing-edlib

Parallelizing the Edlib sequencing library using MCE and OpenMP in Perl

bioinformatics rna-seq sequence-alignment sequencing-rna

Last synced: 26 Mar 2025

https://github.com/chrisarg/bio-seqalignment-components-sundry

Various components for building RNA sequencing applications in Perl

bioinformatics fasta fastq rna-seq sequence-alignment sequencing

Last synced: 26 Mar 2025

https://github.com/nifets/torusevol

This is a Bayesian model for sequence and structure alignment of multiple proteins in a star phylogeny. The structural divergence across time is modelled by letting the dihedral angles of the backbones evolve according to a diffusion over the flat square torus.

bayesian-inference gibbs-sampling monte-carlo-sampling protein-structure sequence-alignment structure-alignment

Last synced: 09 Feb 2026

https://github.com/hhandika/charset-extractor

Extract NEXUS partition blocks from a collection of concatenated alignments

genomics phylogenetics phylogenomics sequence-alignment

Last synced: 01 Jul 2025

https://github.com/lisabensoussan/dna_lab

This project provides hands-on experience in DNA analysis using R, covering sequence manipulation, mutation analysis, GC content, fragment analysis, sequence alignment, RNA-seq, variant analysis, and phylogenetics.

dna-sequences fragment-length gc-content mutation-analysis phylogenetics rna-seq-analysis sequence-alignment

Last synced: 26 Feb 2025

https://github.com/johnedquinn/sequence-align

Project to perform sequence alignment of short DNA sequences of Anopheles Gambiae (common mosquito). This implementation leverages distributed computing through the HTCondor and Work Queue systems to drastically improve the computational runtime. The tool utilized to compute scores of DNA comparisons is swaligntool.

cloud distributed-computing dna htcondor sequence-alignment workqueue

Last synced: 31 Mar 2025

https://github.com/samstan4/pairwise-sequence-alignment-algorithm

An implementation of the pairwise sequence alignment algorithm with an affine gap penalty implemented in C++

algorithms datastructures dynamic-programming genomics matrix sequence-alignment sequence-alignment-visualization

Last synced: 11 Jun 2025

https://github.com/sgtpep/vimsa

The VIM-based multiple sequence alignment (MSA) editor.

bioinformatics fasta msa sequence-alignment vim

Last synced: 20 Mar 2025

https://github.com/chrisarg/bio-seqalignment-components-seqmapping

Components for sequence mapping under the Bio::SeqAlignment namespace

bioinformatics rna-seq rna-seq-analysis rna-sequencing sequence-alignment

Last synced: 26 Mar 2025