Comparative Genomics Python Packages

pycirclize

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

ppanggolin

Build a partitioned pangenome graph from microbial genomes

pygenomeviz

A genome visualization python package for comparative genomics

camsa

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

jcvi

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

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

syntenyqc

A command line app for the pre-processing and quality control of synteny plot neighbourhoods

jlsteenwyk-biokit

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

fastoma

FastOMA is a scalable software package to infer orthology relationship.

cogclassifier

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

aniclustermap

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

funannotate

funannotate: eukaryotic genome annotation pipeline

chess-hic

Quantitative comparison and automatic feature extraction for chromatin contact data.

hyphy-python

HyPhy: Hypothesis testing using Phylogenies

pyrion

A fast and efficient bioinformatics library for genomic data processing

gbkviz

Simple web application to visualize and compare genomes in Genbank files

fastdtlmapper

Fast genome-wide DTL(Duplication-Transfer-Loss) event mapping tool

mgcplotter

Microbial Genome Circular plotting tool for comparative genomics using Circos

scarap

A toolkit for prokaryotic comparative genomics

phenotrex

Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn

pangbank-cli

Command-line tool for retrieving pangenomes using the PanGBank API.

zol

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

hyphy

HyPhy: Hypothesis testing using Phylogenies