multiple-sequence-alignment | Topic

Topic: "multiple-sequence-alignment"

sokrypton/ColabFold

Making Protein folding accessible to all!

Language: Jupyter Notebook - Size: 138 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2,199 - Forks: 537

microsoft/evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Language: Python - Size: 19.7 MB - Last synced at: 1 day ago - Pushed at: 2 months ago - Stars: 576 - Forks: 90

inab/trimal

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

Language: C++ - Size: 56.2 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 203 - Forks: 47

refresh-bio/FAMSA

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

Language: C++ - Size: 12.7 MB - Last synced at: 8 days ago - Pushed at: 7 months ago - Stars: 155 - Forks: 27

moshi4/pyMSAviz

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

Language: Python - Size: 7.2 MB - Last synced at: 9 days ago - Pushed at: 5 months ago - Stars: 124 - Forks: 16

yangao07/abPOA

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

Language: C - Size: 26 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 119 - Forks: 18

diegozea/MIToS.jl

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

Language: Julia - Size: 56.4 MB - Last synced at: 16 days ago - Pushed at: 6 months ago - Stars: 77 - Forks: 17

gcorso/NeuroSEED

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

Language: Python - Size: 1.38 MB - Last synced at: 21 days ago - Pushed at: over 1 year ago - Stars: 72 - Forks: 18

morispi/CONSENT

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

Language: C++ - Size: 15.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 53 - Forks: 4

psipred/DMPfold2

Fast and accurate protein structure prediction

Language: Python - Size: 128 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 49 - Forks: 12

jasperlinthorst/reveal

Graph based multi genome aligner

Language: Python - Size: 6.48 MB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 47 - Forks: 3

elttaes/Revisiting-PLMs

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

Language: Python - Size: 6.55 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 41 - Forks: 9

althonos/pyfamsa

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

Language: Cython - Size: 289 KB - Last synced at: 11 days ago - Pushed at: about 2 months ago - Stars: 31 - Forks: 3

thekaplanlab/msabrowser

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

Language: JavaScript - Size: 412 KB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 31 - Forks: 7

sanderlab/alignmentviewer

Multiple sequence alignment visualizer

Language: JavaScript - Size: 9.26 MB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 30 - Forks: 6

jaswindersingh2/SPOT-RNA2

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

Language: Perl - Size: 185 MB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 25 - Forks: 8

yangao07/TideHunter

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

Language: C - Size: 48.9 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 24 - Forks: 4

althonos/pytrimal

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

Language: Cython - Size: 795 KB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 23 - Forks: 2

vinuesa/TIB-filoinfo

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

Language: Shell - Size: 160 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 21 - Forks: 5

althonos/pymuscle5

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

Language: Cython - Size: 115 KB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 20 - Forks: 2

nanoporetech/pyspoa

Python bindings to spoa

Language: Python - Size: 45.9 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 3

Xinglab/TideHunter

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

Language: C - Size: 48.8 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 18 - Forks: 2

benhid/Sequoya

Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics

Language: Python - Size: 111 MB - Last synced at: 17 days ago - Pushed at: about 5 years ago - Stars: 18 - Forks: 3

LKremer/MSA_trimmer

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

Language: Python - Size: 8.79 KB - Last synced at: 20 days ago - Pushed at: about 6 years ago - Stars: 17 - Forks: 2

amaurypm/pseqsid

Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.

Language: Rust - Size: 81.1 KB - Last synced at: 16 days ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 1

orangeSi/pymsaploter

plot Multiple Sequence Alignment(MSA) of Clustal by python package

Language: HTML - Size: 1.73 MB - Last synced at: 14 days ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 3

Xinglab/abPOA

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

Language: C - Size: 26 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 12 - Forks: 3

krejciadam/hammock

Cluster up to millions of peptide sequences on shared sequence motifs.

Language: Java - Size: 11.1 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 11 - Forks: 2

Bitbol-Lab/DiffPALM

Differentiable Pairing using Alignment-based Language Models

Language: Jupyter Notebook - Size: 2.82 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 2

AndreaGuarracino/WFPOA 📦

An extension to the wavefront algorithm that generalizes it to work on directed acyclic sequence graphs

Language: C - Size: 438 KB - Last synced at: 23 days ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 0

rpianezza/GenomeDelta

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

Language: Shell - Size: 61.7 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 8 - Forks: 0

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.

Language: Python - Size: 9.77 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0

malabz/HAlign-3

do multiple nucleotide sequence alignment fast and accurately

Language: Java - Size: 120 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3

Maryam-Haghani/NEFFy

NEFF Calculator and MSA File Converter

Language: C++ - Size: 3.62 MB - Last synced at: 9 days ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 0

dunhamlab/PacRAT

Improving long-read barcode-variant mapping using multiple sequence alignment.

Language: Python - Size: 8.02 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 4

aadimator/NetMSA.jl

Implementation of the NetMSA algorithm in Julia for multiple sequence alignment problem.

Language: Jupyter Notebook - Size: 142 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

MDU-PHL/arbow 📦

Cultivate your multiple sequence alignments to get better trees

Language: Python - Size: 176 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 1

samberry19/bioviper

Enhancements to Biopython for working with biological data

Language: Jupyter Notebook - Size: 9.94 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 1

MountainMan12/SARS-Cov2-phylo

Analysis of the viral genomes of SARS-CoV2 using MAFFT and igtree

Language: Python - Size: 38.1 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 3

kullrich/MSA2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Language: C++ - Size: 615 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 4 - Forks: 0

zamirmehdi/Bioinformatics-Course

Language: Jupyter Notebook - Size: 30.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

ramonamerong/hladownload

A tool for downloading HLA alleles, epitopes and frequencies

Language: Python - Size: 1.54 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

malabz/HAlign-2

a multiple sequence alignment tool

Language: HTML - Size: 1.6 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 4

malabz/TPMA

⚙️TPMA: a two pointers meta-alignment tool to ensemble different nucleic acid multiple sequence alignment results

Language: C++ - Size: 63.5 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

abacaxiguy/alinhamento-multiplo-dna

🧬 Alinhamento Múltiplo de sequências feito em C, construído na matéria de Estrutura de Dados. 📚

Language: C - Size: 5.3 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

ecolell/pfamserver

PFAM's micro service to assist to Mistic2.

Language: Python - Size: 3.01 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

TurakhiaLab/TWILIGHT

High throughput tool for tall and wide multiple sequence alignment.

Language: C++ - Size: 43.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 1

jonas-fuchs/MSAexplorer

A multiple sequence alignment viewer in your browser!

Language: Python - Size: 47.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 0

malabz/ReAlign-N

🧬ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments

Language: C++ - Size: 104 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 0

extavourlab/Oskar_Evolution

GitHub Repository associated to the study of the evolutionary history and functional inference of the Oskar protein

Language: Turing - Size: 119 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 3

malabz/stmsa-cpp

do multiple nucleotide sequence alignment fast and accurately

Language: C++ - Size: 112 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 1

mohammadtavakoli78/Bioinformatics

This is projects of Bioinformatics

Language: Python - Size: 14.6 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

danielfamiyeh/biothon

Biosequence analysis library

Language: Python - Size: 298 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

clarkevansteenderen/CBC_Tutorials

A collection of phylogenetics tutorials delivered to colleagues at the Centre for Biological Control (CBC). Topics include producing Bayesian and Maximum Likelihood trees, haplotype networks, reading phylogenies into R, analysing ISSR and SSR data, and using STRUCTURE and SplitsTree.

Language: OpenEdge ABL - Size: 73 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0