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

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

camsa

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

jlsteenwyk-biokit

No description available

syntenyqc

Want to make a neighbourhood-scale synteny plot? Have too many genomic neighbourhoods? SyntenyQC may help!

fastoma

FastOMA is a scalable software package to infer orthology relationship.

funannotate

funannotate: eukaryotic genome annotation pipeline

pyrion

Comparative genomics toolkit

gbkviz

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

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

chess-hic

Comparison of Hi-C Experiments using Structural Similarity.

hyphy-python

HyPhy package interface library

fastdtlmapper

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

scarap

A toolkit for prokaryotic comparative genomics

phenotrex

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

mgcplotter

Microbial Genome Circular plotting tool for comparative genomics using Circos

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