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

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

A grammar of graphics for comparative genomics

An analysis and visualization platform for 'omics data

Eukaryotic Genome Annotation Pipeline

A genome visualization python package for comparative genomics

Chromosome visualization for the web

Build a partitioned pangenome graph from microbial genomes

HyPhy: Hypothesis testing using Phylogenies

A fast whole-genome aligner based on de Bruijn graphs

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Genome wide orthology inference and dNdS estimation

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

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

FastOMA is a scalable software package to infer orthology relationship.

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

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

The Ensembl Compara Perl API and SQL schema

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

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.