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Search results for comparative genomics

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57 search results found

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

Gggenomes ⭐ 518

A grammar of graphics for comparative genomics

Pycirclize ⭐ 476

Circular visualization in Python (Circos Plot, Chord Diagram)

An analysis and visualization platform for 'omics data

Ideogram ⭐ 265

Chromosome visualization for the web

Funannotate ⭐ 261

Eukaryotic Genome Annotation Pipeline

Ppanggolin ⭐ 191

Build a partitioned pangenome graph from microbial genomes

Pygenomeviz ⭐ 177

A genome visualization python package for comparative genomics

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

Recentrifuge ⭐ 83

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Orthologr ⭐ 68

Genome wide orthology inference and dNdS estimation

Ensembl Compara ⭐ 46

The Ensembl Compara Perl API and SQL schema

Quota Alignment ⭐ 44

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

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.

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

Aniclustermap ⭐ 38

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

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

Orthogene ⭐ 31

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

Pan-genomic sequence analysis

EzAAI - High Throughput Prokaryotic AAI Calculator

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

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

Cogclassifier ⭐ 27

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

Segalign ⭐ 26

A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC4140

Comparative_genomics ⭐ 24

Micro 612 genomics workshop

Comparison of Hi-C Experiments using Structural Similarity.

Taxon-aware analysis of clustered protein sequences

Compare_genomes ⭐ 23

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

Gssplayground ⭐ 21

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

A tool for analysis of assembly graphs

Mgcplotter ⭐ 20

Microbial Genome Circular plotting tool for comparative genomics using Circos

A toolkit for prokaryotic comparative genomics

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

Cgview_comparison_tool ⭐ 19

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

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

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

Workflow for identifying and classifying homologous gene/protein sequences

Performs MCMCglmm on multiple phylogenetic trees

Compbio Gists ⭐ 12

Computational Biology & Bioinformatics Resources

Syntenet ⭐ 12

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

Plot_genome_align_fig ⭐ 10

Plot genome alignment figure using progressiveMauve & genoPlotR

Positive Selection ⭐ 10

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

FastOMA is a scalable software package to infer orthology relationship.

Digs Tool ⭐ 9

Database-Integrated Genome Screening (DIGS) tool. Explore genomes interactively using BLAST and a relational database.

AccuSyn: An Accurate Web-based Genome Synteny Browser

Gluetools ⭐ 9

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

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

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

Notebooks ⭐ 8

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

Fastdtlmapper ⭐ 7

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

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

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

CAARS: Comparative Assembly and Annotation of RNA-Seq data

Teaching Comp Genomics Vis ⭐ 6

Comparative Genomics and Visualisation teaching module

Fishcomparativeatlas ⭐ 6

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

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

Buscoorthophylo ⭐ 5

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

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