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

zombi2

A Python library for simulating the evolution of species, genomes, sequences and traits

jcvi

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

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

primer-finder

Find group-specific kmers in assembled genomes to design selective (q)PCR assays

camsa

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

fastoma

FastOMA is a scalable software package to infer orthology relationship.

syntenyqc

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

jlsteenwyk-biokit

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

liftassess

Python tool for assessing genomic coordinate liftOver results using exact alignment geometry, UCSC comparative evidence, reverse liftOver and flanking-context checks, and provenance-aware interpretation.

panorama-sys

PANORAMA Project

aniclustermap

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

phagemine

Phage-focused genome annotation and comparative genomics workflow integrating structural gene prediction, evidence-supported functional annotation, and INPHARED nearest-phage analysis.

pyrion

Comparative genomics toolkit

cogclassifier

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

funannotate

Eukaryotic Genome Annotation Pipeline

chess-hic

Comparison of Hi-C Experiments using Structural Similarity.

pangbank-cli

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

hyphy-python

HyPhy: Hypothesis testing using Phylogenies

gbkviz

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

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