Microbial 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

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

treesapp

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

cogclassifier

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

genegrouper

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

aniclustermap

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

gbkviz

Simple web application to visualize and compare genomes in Genbank files

lissero

In silico serotype prediction for Listeria monocytogenes

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

mgcplotter

Microbial Genome Circular plotting tool for comparative genomics using Circos

metasbt

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

albatradis

Comparative TraDIS analysis

biodive

Discovery of k-mer sequences associated with high rates of sequence diversification.

mdu-pytools

Small tools/scripts written in Python for MDU

qiime-tools

Tools for phylogenetic data analysis including visualization and cluster-computing support.

phylotoast

Tools for phylogenetic data analysis including visualization and cluster-computing support.