multiple-sequence-alignment

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sokrypton /ColabFold

Star2.3k

Making Protein folding accessible to all!

bioinformatics protein-structure structure-prediction multiple-sequence-alignment

UpdatedJul 3, 2025
Jupyter Notebook

microsoft /evodiff

Star612

Generation of protein sequences and evolutionary alignments via discrete diffusion models

generative-model protein-sequences multiple-sequence-alignment discrete-diffusion

UpdatedMay 29, 2025
Python

inab /trimal

Star211

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

trimming multiple-sequence-alignment bioinformatics-tool

UpdatedJul 3, 2025
C++

refresh-bio /FAMSA

Star156

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

bioinformatics proteomics longest-common-subsequence pfam multiple-sequence-alignment sequence-similarity guide-tree

UpdatedSep 18, 2024
C++

moshi4 /pyMSAviz

Star133

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

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

UpdatedDec 1, 2024
Python

yangao07 /abPOA

Star124

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

simd long-reads multiple-sequence-alignment partial-order-alignment consensus-sequences banded-dp consensus-sequence alignment-graph gfa-format

UpdatedJul 3, 2025
C

diegozea /MIToS.jl

Star81

A Julia package to analyze protein sequences, structures, and evolutionary information

bioinformatics biology proteins pdb protein-structure julia-language conservation mutual-information structural-bioinformatics protein-evolution pfam sifts multiple-sequence-alignment coevolution protein-sequence-analysis

UpdatedJul 3, 2025
Julia

gcorso /NeuroSEED

Star73

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

machine-learning bioinformatics pytorch biological-sequences hierarchical-clustering multiple-sequence-alignment neurips-2021

UpdatedOct 14, 2023
Python

elttaes /Revisiting-PLMs

Star63

Exploring Evolution-aware & free protein language models as protein function predictors

benchmark pytorch contact-prediction stability multiple-sequence-alignment protein-annotation function-prediction protein-classification alphafold protein-language-model alphafold2 fitness-prediction zero-shot-prediction msa-construction msa-transformer esm1b remote-homology-detection metal-ion-binding

UpdatedSep 28, 2024
Python

morispi /CONSENT

Star55

Scalable long read self-correction and assembly polishing with multiple sequence alignment

assembly ngs consensus correction long self msa reads contigs long-reads multiple-sequence-alignment polishing self-correction

UpdatedFeb 6, 2024
C++

psipred /DMPfold2

Star53

Fast and accurate protein structure prediction

deep-learning end-to-end multiple-sequence-alignment protein-structure-prediction

UpdatedJan 17, 2025
Python

jasperlinthorst /reveal

Star47

Graph based multi genome aligner

genome graph assembly gfa alignment reveal multiple-sequence-alignment

UpdatedSep 17, 2021
Python

thekaplanlab /msabrowser

Star33

🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations

bioinformatics genetics sequence-alignment msa protein-domains multiple-sequence-alignment msa-viewer sequence-alignment-visualization msabrowser

UpdatedMay 21, 2024
JavaScript

althonos /pyfamsa

Star32

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

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

UpdatedJun 16, 2025
Cython

jaswindersingh2 /SPOT-RNA2

Star31

Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning

deep-learning transfer-learning multiple-sequence-alignment rna-secondary-structure canonical-base-pairs pseudoknot-base-pairs lone-pairs direct-coupling-analysis evolutionary-information non-canonical-base-pairs homologous-sequence spot-rna2 base-triples

UpdatedApr 3, 2021
Perl

yangao07 /TideHunter

Star30

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

tandem-repeats long-reads multiple-sequence-alignment seed-and-chain partial-order-alignment

UpdatedJun 17, 2024
C

sanderlab /alignmentviewer

Star29

Multiple sequence alignment visualizer

javascript html js protein alignment sequence-alignment msa multiple-sequence-alignment

UpdatedJan 26, 2023
JavaScript

althonos /pytrimal

Star26

Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!

python bioinformatics genomics python-library simd python-interface cython-wrapper multiple-sequence-alignment alignment-trimming

UpdatedMay 7, 2025
Cython

vinuesa /TIB-filoinfo

Star23

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

bioinformatics tutorials linux-shell phylogenetics model-selection blast maximum-likelihood phylogenomics bioinformatics-scripts bash-scripting pangenomics multiple-sequence-alignment reciprocal-blast-hits

UpdatedApr 23, 2025
Shell

Bitbol-Lab /DiffPALM

Star22

Differentiable Pairing using Alignment-based Language Models

machine-learning bioinformatics protein-sequences language-model protein-protein-interaction multiple-sequence-alignment protein-structure-prediction

UpdatedJan 5, 2024
Jupyter Notebook

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