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

python-circos

python Circos

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

lorax

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

pear-ebi

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

bionick

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

automlsa2

Automated Multi-Locus Sequence Analysis phylogenetic tree construction software

ab12phylo

Integrated pipeline for ML phylogenetic inference from ABI trace and FASTA data

sc-supertree

A supertree method for rooted source trees

phytreeviz

Simple phylogenetic tree visualization python package

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

mycolab

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

phyloki

Annotate phylogenetic trees like never before

taxopedia

Taxonomic trees (cladograms) from Wikipedia-scraped data.

graphlan

GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.

jplaceparser

A python parser for jplace (evolutionary placement) files