comparative-genomics | Topic | Ecosyste.ms: Repos

Topic: "comparative-genomics"

moshi4/pyCirclize

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

Language: Python - Size: 55.8 MB - Last synced at: 5 days ago - Pushed at: about 2 months ago - Stars: 880 - Forks: 52

tanghaibao/jcvi

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

Language: Python - Size: 18.2 MB - Last synced at: 13 days ago - Pushed at: 15 days ago - Stars: 818 - Forks: 190

thackl/gggenomes

A grammar of graphics for comparative genomics

Language: R - Size: 111 MB - Last synced at: 28 days ago - Pushed at: 4 months ago - Stars: 675 - Forks: 66

merenlab/anvio

An analysis and visualization platform for 'omics data

Language: Python - Size: 745 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 470 - Forks: 148

nextgenusfs/funannotate

Eukaryotic Genome Annotation Pipeline

Language: Python - Size: 32.3 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 345 - Forks: 88

moshi4/pyGenomeViz

A genome visualization python package for comparative genomics

Language: Python - Size: 74.9 MB - Last synced at: 2 days ago - Pushed at: 20 days ago - Stars: 330 - Forks: 21

eweitz/ideogram

Chromosome visualization for the web

Language: JavaScript - Size: 156 MB - Last synced at: 5 days ago - Pushed at: 13 days ago - Stars: 300 - Forks: 72

labgem/PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

Language: Python - Size: 133 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 267 - Forks: 31

veg/hyphy

HyPhy: Hypothesis testing using Phylogenies

Language: HyPhy - Size: 57.3 MB - Last synced at: 11 days ago - Pushed at: 18 days ago - Stars: 232 - Forks: 70

medvedevgroup/SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs

Language: C++ - Size: 37.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 142 - Forks: 19

khyox/recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Language: Python - Size: 14.1 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 94 - Forks: 8

drostlab/orthologr

Genome wide orthology inference and dNdS estimation

Language: R - Size: 103 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 90 - Forks: 27

moshi4/ANIclustermap

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

Language: Python - Size: 184 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 80 - Forks: 10

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: 14 days ago - Pushed at: about 1 month ago - Stars: 66 - Forks: 6

Kalan-Lab/zol

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

Language: Python - Size: 83.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 59 - Forks: 4

tanghaibao/quota-alignment

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

Language: Python - Size: 2.96 MB - Last synced at: 2 months ago - Pushed at: over 7 years ago - Stars: 57 - Forks: 20

Ensembl/ensembl-compara

The Ensembl Compara Perl API and SQL schema

Language: Perl - Size: 324 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 52 - Forks: 69

SWittouck/SCARAP

A toolkit for prokaryotic comparative genomics

Language: Python - Size: 238 KB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 49 - Forks: 7

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: 6 months ago - Pushed at: 6 months ago - Stars: 46 - Forks: 7

gsneha26/SegAlign

A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043

Language: C++ - Size: 103 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 45 - Forks: 12

LyonsLab/coge

CoGe (Comparative Genomics) Platform

Language: Perl - Size: 162 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 44 - Forks: 17

legumeinfo/gcv

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

Language: TypeScript - Size: 11.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 43 - Forks: 10

neurogenomics/orthogene

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

Language: R - Size: 7.95 MB - Last synced at: 30 days ago - Pushed at: 3 months ago - Stars: 43 - Forks: 4

chadlaing/Panseq

Pan-genomic sequence analysis

Language: HTML - Size: 16.6 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 43 - Forks: 14

medvedevgroup/TwoPaCo

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

Language: C++ - Size: 11.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 40 - Forks: 10

endixk/ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator

Language: Java - Size: 41.1 MB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 39 - Forks: 4

moshi4/MGCplotter 📦

Microbial Genome Circular plotting tool for comparative genomics using Circos

Language: Python - Size: 68.1 MB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 38 - Forks: 7

alipirani88/Comparative_Genomics

Micro 612 genomics workshop

Language: Shell - Size: 42 MB - Last synced at: 7 months ago - Pushed at: about 4 years ago - Stars: 36 - Forks: 32

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: 11 months ago - Pushed at: almost 5 years ago - Stars: 31 - Forks: 7

almeidasilvaf/syntenet

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

Language: R - Size: 75.3 MB - Last synced at: 29 days ago - Pushed at: 6 months ago - Stars: 30 - Forks: 6

DRL/kinfin

Taxon-aware analysis of clustered protein sequences

Language: Python - Size: 163 MB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 30 - Forks: 12

jeffersonfparil/compare_genomes

A comparative genomics workflow using Nextflow, conda, Julia and R

Language: Nextflow - Size: 1.37 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 29 - Forks: 5

amnh/PCG

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Language: Haskell - Size: 120 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 28 - Forks: 1

paulstothard/cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

Language: Perl - Size: 693 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 27 - Forks: 17

almeidasilvaf/doubletrouble

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

Language: R - Size: 18.7 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 26 - Forks: 0

vaquerizaslab/chess

Comparison of Hi-C Experiments using Structural Similarity.

Language: Python - Size: 241 MB - Last synced at: 10 months ago - Pushed at: almost 2 years ago - Stars: 26 - Forks: 6

compbiol/CAMSA

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Language: Python - Size: 6.46 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 24 - Forks: 4

JLSteenwyk/BioKIT

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

Language: Python - Size: 43.2 MB - Last synced at: about 13 hours ago - Pushed at: 6 months ago - Stars: 21 - Forks: 10

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: about 3 years ago - Stars: 21 - Forks: 4

tanghaibao/mcscan 📦

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Language: C++ - Size: 27.9 MB - Last synced at: 4 months ago - Pushed at: over 14 years ago - Stars: 21 - Forks: 13

laelbarlow/amoebae

Workflow for identifying and classifying homologous gene/protein sequences

Language: Python - Size: 7.72 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 20 - Forks: 2

Kalan-Lab/lsaBGC-Pan

lsaBGC - suite for pan-BGC-omics analysis

Language: Python - Size: 77.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 19 - Forks: 2

DessimozLab/FastOMA

FastOMA is a scalable software package to infer orthology relationship.

Language: Python - Size: 991 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 7

robinvanderlee/positive-selection

Scripts and procedures for detecting positively selected genes and codons in primates

Language: Perl - Size: 169 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 19 - Forks: 16

moshi4/plot_genome_align_fig 📦

Plot genome alignment figure using progressiveMauve & genoPlotR

Language: Python - Size: 37 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 16 - Forks: 4

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: 16 days ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 4

ma-compbio/Phylo-HMRF

Language: Python - Size: 9.11 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 3

PlantDr430/BuscoOrthoPhylo

Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs

Language: Python - Size: 43.9 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 15 - Forks: 4

jananiravi/compbio-gists

Computational Biology & Bioinformatics Resources

Language: Shell - Size: 36.1 KB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 3

jorgenunezsiri/accusyn

AccuSyn: An Accurate Web-based Genome Synteny Browser

Language: JavaScript - Size: 31.8 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 14 - Forks: 2

TGuillerme/mulTree

Performs MCMCglmm on multiple phylogenetic trees

Language: R - Size: 7.44 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 3

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: 5 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 2

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: about 1 month ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 6

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: 39.6 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 10 - Forks: 10

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: about 1 month ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 4

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: 2.63 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 9 - Forks: 5

philippmuench/Donut

Donut: automated Circos visualization of multiple fasta files within a docker image

Language: Shell - Size: 141 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 9 - Forks: 2

giffordlabcvr/DIGS-tool

Database-Integrated Genome Screening (DIGS) tool. Explore the dark genome using BLAST and a relational database.

Language: Perl - Size: 49.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 6

almeidasilvaf/cogeqc

An R package to perform systematic quality checks on comparative genomics analyses

Language: R - Size: 9.46 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0

icaromsc/WGCA

JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes

Language: Python - Size: 629 MB - Last synced at: 15 days ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 2

CarineRey/caars

CAARS: Comparative Assembly and Annotation of RNA-Seq data

Language: Python - Size: 19.9 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 8 - Forks: 4

widdowquinn/Teaching-Comp-Genomics-Vis

Comparative Genomics and Visualisation teaching module

Language: Jupyter Notebook - Size: 322 MB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 8 - Forks: 8

DyogenIBENS/FishComparativeAtlas

FishComparativeAtlas is a pipeline to trace the evolution of sister duplicated chromosomes derived from whole genome duplication in teleost genomes.

Language: Python - Size: 55.1 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

ohdongha/OrthNet

CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology

Language: Python - Size: 176 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 3