althonos/pytrimal

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

Language: Cython - Size: 667 KB - Last synced: about 16 hours ago - Pushed: 2 days ago - Stars: 16 - Forks: 2

diegozea/MIToS.jl

Mutual Information Tools for protein Sequence analysis in Julia

Language: Julia - Size: 48.6 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 64 - Forks: 18

mkayasth/viralGeneClock--codespaces

Python tool for relative mutation rate of different genes across viral strains.

Language: Python - Size: 5.24 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0

psipred/DMPfold2

Fast and accurate protein structure prediction

Language: Python - Size: 128 MB - Last synced: about 23 hours ago - Pushed: 10 months ago - Stars: 45 - Forks: 10

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: 9 days ago - Pushed: 9 days ago - Stars: 17 - Forks: 2

althonos/pyfamsa

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

Language: Python - Size: 127 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 21 - Forks: 2

microsoft/evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Language: Python - Size: 18.3 MB - Last synced: 9 days ago - Pushed: about 1 month ago - Stars: 425 - Forks: 57

cankocagil/BioStatistics

Differential Gene Expression, Phylogenetic tree, Sequence Alignments, Biostatistics, Bioinformatic

Language: R - Size: 3.97 MB - Last synced: 18 days ago - Pushed: almost 3 years ago - Stars: 1 - 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: 87.9 KB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

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: 601 KB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 4 - Forks: 0

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: 24 days ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

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: 12 days ago - Pushed: 18 days ago - Stars: 130 - Forks: 26

yangao07/abPOA

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

Language: C - Size: 25.7 MB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 105 - Forks: 18

samberry19/bioviper

Enhancements to Biopython for working with biological data

Language: Jupyter Notebook - Size: 9.92 MB - Last synced: 22 days ago - Pushed: 26 days ago - Stars: 6 - Forks: 1

aadimator/NetMSA.jl

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

Language: Jupyter Notebook - Size: 142 KB - Last synced: 26 days ago - Pushed: 5 months ago - Stars: 6 - Forks: 0

moshi4/pyMSAviz

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

Language: Python - Size: 7.07 MB - Last synced: 22 days ago - Pushed: 8 months ago - Stars: 65 - Forks: 9

inab/trimal

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

Language: C++ - Size: 70.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 146 - Forks: 39

sanderlab/alignmentviewer

Multiple sequence alignment visualizer

Language: JavaScript - Size: 9.26 MB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 25 - Forks: 6

jovanneste/DeepRL-MSA

Using deep reinforcement learning to solve the multiple sequence alignment problem.

Language: Python - Size: 163 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

plotly/react-msa-viewer

React rerelease of MSAViewer

Language: JavaScript - Size: 958 KB - Last synced: 5 days ago - Pushed: over 2 years ago - Stars: 25 - Forks: 15

benhid/Sequoya

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

Language: Python - Size: 111 MB - Last synced: 11 days ago - Pushed: about 4 years ago - Stars: 17 - Forks: 3

rrouz/AncFlow

AncFlow: A snakemake based pipeline for the ancestral sequence reconstruction of clustered phylogenetic subtrees.

Language: Python - Size: 4.64 MB - Last synced: 30 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

dunhamlab/PacRAT

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

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

clabe-wekesa/SATO

A python pipeline that brings together tools for generation of consensus sequence, multiple sequence alignment, and phylogenetic analysis.

Language: Python - Size: 2.16 MB - Last synced: 19 days ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

rpianezza/GenomeDelta

Library-free horizontal transfer detection, with a focus on transposable element invasions

Language: Shell - Size: 54.5 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 4 - Forks: 0

Xinglab/abPOA

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

Language: C - Size: 26 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 12 - Forks: 3

thekaplanlab/msabrowser

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

Language: JavaScript - Size: 412 KB - Last synced: 2 months ago - Pushed: almost 2 years ago - Stars: 29 - Forks: 6

timweh/MEMSA

Multiple sequence alignment tool that builds on the concept of seed-and-extend algorithms

Language: C++ - Size: 154 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

lemora/msa-proteoform-profiler

Detect and annotate proteoforms/domains from RNA-Seq multiple sequence alignments

Language: Python - Size: 200 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

gcorso/NeuroSEED

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

Language: Python - Size: 1.38 MB - Last synced: 11 days ago - Pushed: 7 months ago - Stars: 66 - Forks: 16

orangeSi/pymsaploter

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

Language: HTML - Size: 1.73 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 3

jasperlinthorst/reveal

Graph based multi genome aligner

Language: Python - Size: 6.48 MB - Last synced: 13 days ago - Pushed: over 2 years ago - Stars: 43 - Forks: 3

morispi/CONSENT

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

Language: C++ - Size: 15.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 53 - Forks: 4

Mahaprabu09/DailyFiveCodes2-Nov-2022

Language: Java - Size: 2.93 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

vinuesa/TIB-filoinfo

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

Language: Shell - Size: 155 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 16 - Forks: 4

Bitbol-Lab/DiffPALM

Differentiable Pairing using Alignment-based Language Models

Language: Jupyter Notebook - Size: 2.82 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 10 - Forks: 2

LKremer/MSA_trimmer

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

Language: Python - Size: 8.79 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 13 - Forks: 1

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: about 2 months ago - Pushed: 10 months ago - Stars: 17 - Forks: 2

zamirmehdi/Bioinformatics-Course

Language: Jupyter Notebook - Size: 30.1 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 0

arminZolfaghari/Bioinformatics-Course-Assignments

Bioinformatic Course - Programming Assignments - Winter 2022

Language: Python - Size: 18.6 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - 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: 7 months ago - Pushed: 7 months ago - Stars: 8 - Forks: 0

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: 9 days ago - Pushed: 3 months ago - Stars: 11 - Forks: 1

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: 6 months ago - Pushed: 6 months ago - Stars: 22 - Forks: 5

malabz/HAlign-2

a multiple sequence alignment tool

Language: HTML - Size: 1.6 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 4

desi109/SARS-Cov-2-gene-3-multiple-sequence-alignment

Course project: Bioinformatics (BIO) ➟ Multiple sequence alignment of 10 genetic sequences of SARS-2 (gene 3) – T-Coffee

Size: 60.4 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 0 - 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: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

bioinfweb/LibrAlign

A Java GUI library for displaying and editing multiple sequence alignments and attached raw- and metadata

Language: Java - Size: 13.1 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

bioinfweb/AlignmentComparator

Visualizing differences between alternative multiple sequence alignments of the same dataset

Language: Java - Size: 10.8 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

hamalcij/biotool

Bioinformatics Toolbox

Language: C++ - Size: 406 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

maingoc303/Graph_Genome

Language: HTML - Size: 14.8 MB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 0 - 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: 9 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 3

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: 9 months ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

merlyescalona/gacmsa

GACMSA: Get Allele counts from Multiple Sequence Alignment files

Language: Python - Size: 112 KB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

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: 7 months ago - Pushed: about 3 years ago - Stars: 20 - Forks: 7

morioka/alphamalig

ALPHAMALIG(ALPHAbet Multiple ALIGnment)

Language: C - Size: 283 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

fadyehabamer/BioInformatics-SandBox

Bio Informatics Lecture Notes @ Faculty of computer and information Sciences ' MU ' for the '4th Year' IT Department

Size: 3.91 MB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

elttaes/Revisiting-PLMs

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

Language: Python - Size: 6.55 MB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 41 - Forks: 9

MountainMan12/SARS-Cov2-phylo

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

Language: Python - Size: 38.1 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 3

krejciadam/hammock

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

Language: Java - Size: 11.1 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 11 - Forks: 2

nanoporetech/pyspoa

Python bindings to spoa

Language: Python - Size: 45.9 KB - Last synced: 8 days ago - Pushed: 8 months ago - Stars: 12 - Forks: 3

ramonamerong/hladownload

A tool for downloading HLA alleles, epitopes and frequencies

Language: Python - Size: 1.54 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 3 - Forks: 1

danielfamiyeh/biothon

Biosequence analysis library

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

MDU-PHL/arbow 📦

Cultivate your multiple sequence alignments to get better trees

Language: Python - Size: 176 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 6 - Forks: 1

Old-Shatterhand/MSADRL

(Deep) Reinforcement Learning Framework to align multiple sequences.

Language: Python - Size: 111 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

malabz/stmsa-cpp

do multiple nucleotide sequence alignment fast and accurately

Language: C++ - Size: 112 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 1

mohammadtavakoli78/Bioinformatics

This is projects of Bioinformatics

Language: Python - Size: 14.6 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

malabz/HAlign-3

do multiple nucleotide sequence alignment fast and accurately

Language: Java - Size: 120 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 8 - Forks: 3

matchy-at-ethz/22hs-comp-bio

2022 Herbstsemester Computational Biology @ ETHz

Size: 3.91 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

ecolell/pfamserver

PFAM's micro service to assist to Mistic2.

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

kloetzl/mugsy

Mugsy - multiple whole genome alignment tool

Language: C++ - Size: 22.3 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 2 - Forks: 1

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: 10 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 0

MountainMan12/GISAID_phylo

COVID-19 mortality risk assessment among various age groups using phylogenomic analysis

Language: R - Size: 1.46 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 4

AmitMandliya/multiple-sequence-alignment

Applying nature inspired ant colony optimization algorithm to solve the multiple sequence alignment problem in Julia language.

Language: Jupyter Notebook - Size: 854 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 2

bioinfweb/PhyDE2

An alignment editor for phylogenetic purposes

Language: Java - Size: 7.03 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

rajathpatel23/dna_sequencing_algo

Comparative Analysis of DNA sequencing Algorithm

Language: Shell - Size: 1.43 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

hitbc/TideHunter

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

Language: C - Size: 435 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

arzwa/pal2cal

yes indeed

Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

mcm2020/average-maxZ-score

A statistical measure for gauging the polymorphic extent of sequences in a multiple sequence alignment.

Language: Python - Size: 72.3 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0