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

primer-finder

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

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

camsa

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

fastoma

FastOMA is a scalable software package to infer orthology relationship.

syntenyqc

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

jlsteenwyk-biokit

No description available

liftassess

Assessment of genomic coordinate liftOver mappings with exact geometry and provenance

cogclassifier

A tool for classifying prokaryote protein sequences into COG functional category

funannotate

Eukaryotic Genome Annotation Pipeline

panorama-sys

Comparative pangenomic analysis toolbox

aniclustermap

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

phagemine

Evidence-first phage annotation and discovery mining

pyrion

A fast and efficient bioinformatics library for genomic data processing

chess-hic

Quantitative comparison and automatic feature extraction for chromatin contact data.

pangbank-cli

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

hyphy-python

HyPhy package interface library

gbkviz

Simple web application to visualize and compare genomes in Genbank files

fastdtlmapper

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

phenotrex

Microbial Phenotype Prediction