Phylogenetic Trees Python Packages

pycirclize

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

cogent3

Comparative Genomics Toolkit 3

itolapi

Python API for the Interactive Tree of Life (iTOL)

phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

pear-ebi

Calculates distances of trees in large collections. Embeds distances and plot the embeddings with dynamic interfaces.

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

genome-comparator

Fast genome comparison with Mash, from assemblies or reads: distance matrix, UPGMA/NJ/ME trees with bootstrap support, and interactive PCoA

lorax

a web server that "speaks for the (phylogenetic) trees"

bionick

Software for manipulating Newick strings and adding phylogenies to Matplotlib visuals.

python-circos

python Circos

ab12phylo

AB12PHYLO: An integrated easy-to-use pipeline for ML phylogenetic tree inference

automlsa2

Automated Multi-Locus Sequence Analysis phylogenetic tree construction software

dotanglegram

Python implementation of the Displacement-Optimized (DO) Tanglegram algorithm for phylogenetic trees

sc-supertree

A supertree method for rooted source trees

phytreeviz

Simple phylogenetic tree visualization python package for phylogenetic analysis

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

taxopedia

Taxonomic trees (cladograms) from Wikipedia-scraped data.

mycolab

Suite of mycology applications and tools for automating common lab workflows.

phyloki

🌳Tool to fetch seqs metadata from NCBI to annotate phylogenetic trees

graphlan

High-quality circular representations of taxonomic and phylogenetic trees

jplaceparser

A python parser for jplace (evolutionary placement) files