GitHub topics: comparative-genomics

Repositories

merenlab/anvio

An analysis and visualization platform for 'omics data

Language: Python - Size: 774 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 484 - Forks: 150

drostlab/orthologr

Genome wide orthology inference and dNdS estimation

Language: R - Size: 103 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 96 - Forks: 29

mateomics/babesia_genomic_analysis

Proyecto de BioPython, Sem3, LCG. Análisis de genómica comparativa y funcional de *Babesia divergens*

Size: 2.96 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

JRaviLab/compbio-gists

Computational Biology & Bioinformatics Resources

Language: Shell - Size: 39.1 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 15 - Forks: 4

moshi4/pyCirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

Language: Python - Size: 62.3 MB - Last synced at: 1 day ago - Pushed at: 7 days ago - Stars: 955 - Forks: 51

This repository provides an easy-to-use Python-based pipeline for reconstructing phylogenetic trees from whole bacterial genomes. It automates the process of identifying orthologous single-copy genes, aligning sequences, trimming alignments, and generating a concatenated supermatrix ready for phylogenetic analysis. The pipeline requires only .fasta

Language: Python - Size: 6.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2 - Forks: 0

moshi4/ANIclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

Language: Python - Size: 184 MB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 85 - Forks: 10

tanghaibao/jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

Language: Python - Size: 18.2 MB - Last synced at: 1 day ago - Pushed at: 14 days ago - Stars: 850 - Forks: 195

veg/hyphy

HyPhy: Hypothesis testing using Phylogenies

Language: HyPhy - Size: 57.9 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 239 - Forks: 69

satoshikawato/gbdraw

A genome diagram generator for microbes and organelles

Language: Python - Size: 566 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 15 - Forks: 4

moshi4/pyGenomeViz

A genome visualization python package for comparative genomics

Language: Python - Size: 75.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 357 - Forks: 21

Kalan-Lab/zol

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Language: Python - Size: 97.4 MB - Last synced at: 1 day ago - Pushed at: 10 days ago - Stars: 62 - Forks: 4

Ensembl/ensembl-compara

The Ensembl Compara Perl API and SQL schema

Language: Perl - Size: 324 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 54 - Forks: 70

moshi4/COGclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Language: Python - Size: 33.6 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 71 - Forks: 6

Martinaa1408/AG_project

This project focuses on the hybrid genome and transcriptome analysis of compost-derived fungal isolates with bioplastic-degrading potential. It delivers high-quality Nanopore + Illumina assemblies, functional annotation, and RNA-Seq profiling to identify PLA/PHA-degrading enzymes supporting environmental biotechnology.

Size: 49.2 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

LucoDevro/CAGEcleaner

A tool to remove genomic redundancy from cblaster gene cluster hits

Language: Python - Size: 174 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 4 - Forks: 0

labgem/PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

Language: Python - Size: 134 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 276 - Forks: 31

kirilenkobm/pyrion

Comparative genomics toolkit

Language: Python - Size: 95.7 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 0 - Forks: 0

DessimozLab/FastOMA

FastOMA is a scalable software package to infer orthology relationship.

Language: Python - Size: 2.31 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 79 - Forks: 16

giffordlabcvr/gluetools

An open, platform-independent software toolkit for storage and interpretation of sequence data, implemented in Java.

Language: Java - Size: 71.6 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 12 - Forks: 2

almeidasilvaf/doubletrouble

An R package to identify and classify duplicated genes from whole-genome protein sequence data

Language: R - Size: 19.3 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 0

JRaviLab/jravilab.github.io

Janani Ravi's Research Group

Language: HTML - Size: 442 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 5

nf-core/pairgenomealign

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

Language: Nextflow - Size: 3.26 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 9 - Forks: 5

endixk/ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator

Language: Java - Size: 97 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 44 - Forks: 5

khyox/recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Language: Python - Size: 14.1 MB - Last synced at: 11 days ago - Pushed at: 4 months ago - Stars: 96 - Forks: 8

Kalan-Lab/lsaBGC-Pan

lsaBGC - suite for pan-BGC-omics analysis

Language: Python - Size: 77.6 MB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 20 - Forks: 2

nextgenusfs/funannotate

Eukaryotic Genome Annotation Pipeline

Language: Python - Size: 32.5 MB - Last synced at: 1 day ago - Pushed at: 2 months ago - Stars: 361 - Forks: 88

almeidasilvaf/syntenet

An R package to infer and analyze synteny networks from protein sequences

Language: R - Size: 78 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 30 - Forks: 6

giffordlabcvr/NCBI-RABV-GLUE

Extension to RABV-GLUE capturing NCBI data.

Language: JavaScript - Size: 72 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

thackl/gggenomes

A grammar of graphics for comparative genomics

Language: R - Size: 112 MB - Last synced at: 22 days ago - Pushed at: 2 months ago - Stars: 690 - Forks: 68

oist/GenomicBreaks

Pairwise Alignment Breakpoint Analysis

Language: R - Size: 19.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 3

EBI-Metagenomics/notebooks

MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)

Language: Jupyter Notebook - Size: 43.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 10

vaquerizaslab/chess

Comparison of Hi-C Experiments using Structural Similarity.

Language: Python - Size: 241 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 27 - Forks: 6

almeidasilvaf/rplaza

An R interface to the PLAZA database for plant comparative genomics

Language: R - Size: 1.33 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

moshi4/FastDTLmapper 📦

Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method

Language: Python - Size: 38.9 MB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4

univieCUBE/phenotrex Fork of LokiLuciferase/phenotrex

Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn

Language: Python - Size: 28.3 MB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 11 - Forks: 4

SWittouck/SCARAP

A toolkit for prokaryotic comparative genomics

Language: Python - Size: 238 KB - Last synced at: 3 days ago - Pushed at: 8 months ago - Stars: 50 - Forks: 7

eweitz/ideogram

Chromosome visualization for the web

Language: JavaScript - Size: 156 MB - Last synced at: 29 days ago - Pushed at: 4 months ago - Stars: 303 - Forks: 74

neurogenomics/orthogene

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

Language: R - Size: 7.95 MB - Last synced at: 26 days ago - Pushed at: 6 months ago - Stars: 44 - Forks: 4

medvedevgroup/SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs

Language: C++ - Size: 37.3 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 151 - Forks: 19

Marine-Omics-and-Technology-Lab/ComparativeGenomics

Shell script performing large scale genomics comparisons between 7 genomes using RagTag, Blast and Artemis.

Language: Shell - Size: 487 KB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1

makovalab-psu/mapsea

Mapping And Prediction of Shared Elements in Alignments

Language: Python - Size: 18.5 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

giffordlabcvr/CRESS-GLUE

A GLUE project for comparative genomic analysis of circular Rep-encoding single-stranded DNA (CRESS DNA) viruses

Language: JavaScript - Size: 32.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

giffordlabcvr/Deltaretrovirus-GLUE

A GLUE project for Deltaretroviruses

Language: JavaScript - Size: 13 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

giffordlabcvr/Lentivirus-GLUE

A GLUE project for Lentiviruses (genus Lentivirus)

Language: JavaScript - Size: 44.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

giffordlabcvr/Flavivirus-GLUE

A GLUE project for comparative genomic analysis of flaviviruses

Language: JavaScript - Size: 46.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

NIGMS/Comparative-Microbial-Genomics

In this module, you will learn how sequencing data is generated and go through a detailed guide on assembling, assessing, and annotating a bacterial genome. You will then automate the workflow and perform a large-scale comparative genomic analysis.

Language: Jupyter Notebook - Size: 28.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

legumeinfo/gcv

Federating genomes with love (and synteny derived from functional annotations)

Language: TypeScript - Size: 11.9 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 43 - Forks: 10

carpentries-incubator/topological-data-analysis

Topological data analysis for Comparative Genomics

Language: Python - Size: 10.3 MB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 2 - Forks: 3

moshi4/GBKviz 📦

Easy-to-use web application for visualization and comparison of genomes in Genbank file

Language: Python - Size: 5.25 MB - Last synced at: 14 days ago - Pushed at: over 3 years ago - Stars: 21 - Forks: 4

TGuillerme/mulTree

Performs MCMCglmm on multiple phylogenetic trees

Language: R - Size: 7.44 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 3

Rowena-h/StarshipTrees

Scripts for Hill et al. (2025) doi:10.1093/g3journal/jkaf082 🚀

Language: R - Size: 8.39 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

Rowena-h/GaeumannomycesGenomics

Scripts for Hill et al. (2025) doi:10.1186/s12864-025-11432-0 🌾

Language: R - Size: 3.83 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 0

PalMuc/congeneric_synteny

analysis of synteny across animals

Language: Python - Size: 86 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

alipirani88/Comparative_Genomics

Micro 612 genomics workshop

Language: Shell - Size: 42 MB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 37 - Forks: 32

tanghaibao/quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Language: Python - Size: 2.96 MB - Last synced at: 5 months ago - Pushed at: about 8 years ago - Stars: 57 - Forks: 20

moshi4/MGCplotter 📦

Microbial Genome Circular plotting tool for comparative genomics using Circos

Language: Python - Size: 68.1 MB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 38 - Forks: 7

medvedevgroup/TwoPaCo

A fast constructor of the compressed de Bruijn graph from many genomes

Language: C++ - Size: 11.7 MB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 40 - Forks: 10

Abrar2652/oist-comparative-genomics

Language: Python - Size: 2.36 GB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

giffordlabcvr/IFNL-Evolution

Resources supporting comparative and phylogenetic analysis of IFNL genes

Language: JavaScript - Size: 6.36 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

laelbarlow/amoebae

Workflow for identifying and classifying homologous gene/protein sequences

Language: Python - Size: 7.72 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 20 - Forks: 2

giffordlabcvr/Parvovirus-GLUE

A GLUE project for comparative genomic analysis of parvoviruses

Language: JavaScript - Size: 50.4 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

grigsbyanthony/IW-CGA

A comparative genomic analysis of several Ignatzschineriaceae spp.

Language: R - Size: 3.71 MB - Last synced at: 9 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

JLSteenwyk/BioKIT

a versatile toolkit for processing and analyzing diverse types of sequence data

Language: Python - Size: 43.2 MB - Last synced at: 7 days ago - Pushed at: 9 months ago - Stars: 21 - Forks: 10

josuebarrera/GenEra

genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.

Language: Shell - Size: 74.9 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 46 - Forks: 7

giffordlabcvr/HEV-GLUE

A GLUE project for Hepatitis E Virus (HEV)

Language: HTML - Size: 13.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

seqcode/cross-species-domain-adaptation

Codebase for the domain adaptation (cross-species TF binding prediction) project.

Language: Jupyter Notebook - Size: 37.7 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 12 - Forks: 6

giffordlabcvr/BTV-GLUE

A GLUE project for Bluetongue Virus

Language: JavaScript - Size: 43.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

oist/plessy_pairwiseGenomeComparison

Draft workflow for pairwise genome comparison. We recommend you use the new nf-core version instead: https://nf-cor.e/pairgenomealign

Language: Nextflow - Size: 873 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 4 - Forks: 3

mptrsen/mobilome

TE annotation pipeline and analysis scripts for the insect mobilome publication by Petersen et al.

Language: Perl - Size: 33.2 KB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 3

DRL/kinfin

Taxon-aware analysis of clustered protein sequences

Language: Python - Size: 163 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 30 - Forks: 12

giffordlabcvr/Hepadnaviridae-GLUE

A GLUE project for hepadnaviruses (family Hepadnaviridae)

Language: JavaScript - Size: 37.7 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

gpmerola/Auto-dN-dS

Automate the retrieval, alignment, and dN/dS calculation of the whole CDS sequences across species.

Language: Python - Size: 469 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

vargasrichards/enblastertools

tools for modular, extensible retrieval, filtering & analysis of Ensembl BLAST results

Language: Python - Size: 9.47 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

JuseTiZ/PyScript-for-CT

Python scripts for CT(comparative transcriptomics), PT(phylotranscriptomics) and CG(comparative genomics).

Language: Python - Size: 569 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 1

seninp-bioinfo/MetaComp

Toolkit for comparative metagenomics in EDGE

Language: R - Size: 17.5 MB - Last synced at: 16 days ago - Pushed at: about 7 years ago - Stars: 4 - Forks: 2

vargasrichards/ensembl-blast-tools

Simple tools for retrieval and basic analysis of Ensembl plants BLAST results

Language: Python - Size: 7.88 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

widdowquinn/Teaching-Comp-Genomics-Vis

Comparative Genomics and Visualisation teaching module

Language: Jupyter Notebook - Size: 322 MB - Last synced at: 5 months ago - Pushed at: almost 8 years ago - Stars: 8 - Forks: 8

cgenomicslab/cgenomicslab_green

Source Code for cgenomicslab webpage

Language: HTML - Size: 4.28 MB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ladyson1806/NKR_lifespan

GitHub Repository associated to the study of H. glaber and M.musculus shared proteome for understanding their difference in maximum lifespan [ Hussin Lab, Université de Montréal ]

Language: Jupyter Notebook - Size: 67.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

orangeSi/GSSplayground 📦

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

Language: HTML - Size: 148 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 31 - Forks: 7