comparative-genomics
There are 21 repositories under comparative-genomics topic.
tanghaibao / jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
Language:Python 720- pyCirclize
moshi4 / pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Language:Python 677 - Language:R 572
- anvioLanguage:Python 415
nextgenusfs / funannotate
Eukaryotic Genome Annotation Pipeline
Language:Python 311- Language:JavaScript 282
- pyGenomeViz
A genome visualization python package for comparative genomics
Language:Python 254 - PPanGGOLiN
labgem / PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
Language:Python 230 - Language:HyPhy 201
medvedevgroup / SibeliaZ
A fast whole-genome aligner based on de Bruijn graphs
Language:C++ 137- recentrifuge
khyox / recentrifuge
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Language:Python 86 - Language:R 84
gsneha26 / SegAlign
A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043
Language:C++ 65- ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
Language:Python 62 Guided synteny alignment between duplicated genomes (within specified quota constraint)
Language:Python 54Ensembl / ensembl-compara
The Ensembl Compara Perl API and SQL schema
Language:Perl 51josuebarrera / 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 45- Language:Perl 44
- COGclassifier
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Language:Python 44 - Language:HTML 43
Kalan-Lab / zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Language:Python 43A fast constructor of the compressed de Bruijn graph from many genomes
Language:C++ 39- orthogene
neurogenomics / orthogene
๐งฌ o r t h o g e n e ๐งฌโจโจโจโจโจโจโจ Interspecies gene mappingโจโจโจโจโจ ๐ฆ ๐ ๐ฑ ๐ ๐ณ ๐ ๐ ๐ ๐ ๐ ๐ชฑ ๐ ๐ชฐ ๐ ๐ ๐ ๐ฆ ๐ ๐ ๐ ๐ฆ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ ๐ฆง ๐ ๐ฆ ๐ ๐โโ๏ธ
Language:R 39 legumeinfo / gcv
Federating genomes with love (and synteny derived from functional annotations)
Language:TypeScript 38alipirani88 / Comparative_Genomics
Micro 612 genomics workshop
Language:Shell 36- MGCplotter
Microbial Genome Circular plotting tool for comparative genomics using Circos
Language:Python 34 - Language:Java 32
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 31jeffersonfparil / compare_genomes
A comparative genomics workflow using Nextflow, conda, Julia and R
Language:Nextflow 30- Language:Python 29
paulstothard / cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
Language:Perl 29amnh / PCG
๐๐๐ฎ๐ก๐ค๐๐๐ฃ๐๐ฉ๐๐ ๐พ๐ค๐ข๐ฅ๐ค๐ฃ๐๐ฃ๐ฉ ๐๐ง๐๐ฅ๐ โธบ Haskell program and libraries for general phylogenetic graph search
Language:Haskell 28vaquerizaslab / chess
Comparison of Hi-C Experiments using Structural Similarity.
Language:Python 26- Language:Python 25
- Language:Python 24
DessimozLab / FastOMA
FastOMA is a scalable software package to infer orthology relationship.
Language:Python 21
