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)

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

The Ensembl Compara Perl API and SQL schema

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.