Comparative Genomics Python Packages

pygenomeviz

A genome visualization python package for comparative genomics

pycirclize

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

ppanggolin

Build a partitioned pangenome graph from microbial genomes

jcvi

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

camsa

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

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

cogclassifier

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

syntenyqc

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

jlsteenwyk-biokit

No description available

fastoma

FastOMA is a scalable software package to infer orthology relationship.

pangbank-cli

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

aniclustermap

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

funannotate

funannotate: eukaryotic genome annotation pipeline

pyrion

Comparative genomics toolkit

gbkviz

Simple web application to visualize and compare genomes in Genbank files

chess-hic

Quantitative comparison and automatic feature extraction for chromatin contact data.

hyphy-python

HyPhy: Hypothesis testing using Phylogenies

fastdtlmapper

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

phenotrex

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

scarap

A toolkit for prokaryotic comparative genomics

mgcplotter

Microbial Genome Circular plotting tool using Circos

zol

No description available

hyphy

HyPhy: Hypothesis testing using Phylogenies