multiple-sequence-alignment

There are 5 repositories under multiple-sequence-alignment topic.

ColabFold
sokrypton / ColabFold
Making Protein folding accessible to all!
bioinformatics multiple-sequence-alignment protein-structure structure-prediction
Language:Jupyter Notebook 1818
microsoft / evodiff
Generation of protein sequences and evolutionary alignments via discrete diffusion models
discrete-diffusion generative-model multiple-sequence-alignment protein-sequences
Language:Python 453
inab / trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
bioinformatics-tool multiple-sequence-alignment trimming
Language:C++ 162
refresh-bio / FAMSA
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
bioinformatics multiple-sequence-alignment proteomics longest-common-subsequence pfam guide-tree sequence-similarity
Language:C 140
yangao07 / abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
simd partial-order-alignment banded-dp long-reads consensus-sequences multiple-sequence-alignment alignment-graph consensus-sequence gfa-format
Language:C 113
pyMSAviz
moshi4 / pyMSAviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
bioinformatics matplotlib msa python sequence-analysis visualization genomics multiple-sequence-alignment sequence-alignment
Language:Python 75
diegozea / MIToS.jl
A Julia package to analyze protein sequences, structures, and evolutionary information
bioinformatics protein-sequence-analysis protein-structure protein-evolution coevolution mutual-information conservation structural-bioinformatics pfam pdb sifts multiple-sequence-alignment julia-language biology proteins
Language:Julia 73
gcorso / NeuroSEED
Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)
machine-learning bioinformatics biological-sequences pytorch hierarchical-clustering multiple-sequence-alignment neurips-2021
Language:Python 68
elttaes / Revisiting-PLMs
Exploring Evolution-aware & free protein language models as protein function predictors
alphafold function-prediction fitness-prediction alphafold2 benchmark contact-prediction multiple-sequence-alignment protein-annotation protein-classification protein-language-model pytorch stability esm1b metal-ion-binding msa-construction msa-transformer remote-homology-detection zero-shot-prediction
Language:Python 56
morispi / CONSENT
Scalable long read self-correction and assembly polishing with multiple sequence alignment
ngs correction long-reads long reads self-correction self msa multiple-sequence-alignment consensus contigs assembly polishing
Language:C++ 55
psipred / DMPfold2
Fast and accurate protein structure prediction
protein-structure-prediction deep-learning multiple-sequence-alignment end-to-end
Language:Python 47
jasperlinthorst / reveal
Graph based multi genome aligner
gfa graph alignment genome assembly reveal multiple-sequence-alignment
Language:Python 44
thekaplanlab / msabrowser
🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
bioinformatics genetics msa msa-viewer msabrowser multiple-sequence-alignment protein-domains sequence-alignment sequence-alignment-visualization
Language:JavaScript 30
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
Language:Python 27
sanderlab / alignmentviewer
Multiple sequence alignment visualizer
protein alignment msa javascript js html multiple-sequence-alignment sequence-alignment
Language:JavaScript 26
yangao07 / TideHunter
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
long-reads seed-and-chain multiple-sequence-alignment partial-order-alignment tandem-repeats
Language:C 25
jaswindersingh2 / SPOT-RNA2
Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning
rna-secondary-structure deep-learning evolutionary-information multiple-sequence-alignment homologous-sequence spot-rna2 canonical-base-pairs non-canonical-base-pairs pseudoknot-base-pairs lone-pairs base-triples direct-coupling-analysis transfer-learning
Language:Perl 24
althonos / pytrimal
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!
alignment-trimming bioinformatics cython-wrapper genomics multiple-sequence-alignment python python-interface python-library simd
Language:Cython 20
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
Language:Cython 18
vinuesa / TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
bash-scripting bioinformatics-scripts blast linux-shell maximum-likelihood model-selection multiple-sequence-alignment phylogenetics reciprocal-blast-hits tutorials bioinformatics pangenomics phylogenomics
Language:Shell 18
Xinglab / TideHunter
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
tandem-repeats long-reads seed-and-chain multiple-sequence-alignment partial-order-alignment nanopore-sequencing
Language:C 18
benhid / Sequoya
Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics
metaheuristics optimization sequence-alignments msa multiple-sequence-alignment python
Language:Python 17
DiffPALM
Bitbol-Lab / DiffPALM
Differentiable Pairing using Alignment-based Language Models
bioinformatics language-model machine-learning multiple-sequence-alignment protein-protein-interaction protein-sequences protein-structure-prediction
Language:Jupyter Notebook 17
LKremer / MSA_trimmer
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
sequence-alignment msa-trimmer aligned-regions multiple-sequence-alignment trimming trimmer alignment-trimming cds-alignment codon-alignment phylogenetics paml codeml molecular-evolution
Language:Python 16
nanoporetech / pyspoa
Python bindings to spoa
poa alignment nanopore multiple-sequence-alignment
Language:Python 16
malabz / HAlign-3
do multiple nucleotide sequence alignment fast and accurately
halign multiple-sequence-alignment
Language:Java 13
amaurypm / pseqsid
Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.
identity multiple-sequence-alignment normalized-similarity-score protein-sequences similarity
Language:Rust 12
orangeSi / pymsaploter
plot Multiple Sequence Alignment(MSA) of Clustal by python package
multiple-sequence-alignment python3 svg visualization
Language:HTML 12
Xinglab / abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
consensus-sequence banded-dp simd partial-order-alignment multiple-sequence-alignment long-reads
Language:C 12
krejciadam / hammock
Cluster up to millions of peptide sequences on shared sequence motifs.
bioinformatics java clustering sequence-clustering multiple-sequence-alignment phage-display
Language:Java 11
AndreaGuarracino / WFPOA
An extension to the wavefront algorithm that generalizes it to work on directed acyclic sequence graphs
wfa partial-order-alignment wavefront alignment multiple-sequence-alignment msa consensus-sequences
Language:C 9
zahrasalarian / Bioinformatics-Projects
Several small Bioinformatics projects implementing related algorithms, including Semi-Global alignment, Multiple Sequence Alignment using Star-Alignment, and MSA using PSSM profiles considering Gaps.
bioinformatics multiple-sequence-alignment pssm semi-global-alignments
Language:Python 9
PacRAT
dunhamlab / PacRAT
Improving long-read barcode-variant mapping using multiple sequence alignment.
bioinformatics pacbio multiple-sequence-alignment
Language:Python 7
rpianezza / GenomeDelta
Library-free horizontal transfer detection, with a focus on transposable element invasions
bedtools bwa-mem consensus-sequences fasta fastq genome genome-analysis genome-assembly multiple-sequence-alignment samtools transposable-element transposons
Language:Shell 7
aadimator / NetMSA.jl
Implementation of the NetMSA algorithm in Julia for multiple sequence alignment problem.
julia msa multiple-sequence-alignment particle-swarm-optimization pso
Language:Jupyter Notebook 6
malabz / TPMA
⚙️TPMA: a two pointers meta-alignment tool to ensemble different nucleic acid multiple sequence alignment results
refinement multiple-sequence-alignment meta-alignment
Language:C++ 6