PyiTOL Documentation

PyiTOL is a Python-based, full-pipeline automation command-line tool for iTOL (Interactive Tree of Life) visualization.

Documentation Navigation

Document	Description
Complete CLI Reference	Detailed description of all commands and parameters
API Usage Guide	iTOL API interaction and automated upload/export
Quick Start Tutorial	A 10-minute tutorial from installation to figure output
Taxonomy Analysis Tutorial	Monophyly detection and taxonomy information extraction
Template Generation Tutorial	Generation guide for 31 iTOL v7 template types (plus the external-shape-bubble variant)

Core Features

PyiTOL Feature System:
├── Tree Structure
│   ├── Collapse Clades
│   ├── Prune Tree
│   ├── Node Spacing
│   └── Node Labels
├── Annotation
│   ├── Labels & Popup Info
│   ├── Tree Colors
│   ├── Branch Gradients
│   └── Colored Ranges
├── Datasets
│   ├── Binary Data
│   ├── Simple Bar / Multibar
│   ├── Pie Chart
│   ├── Color Strip
│   ├── Heatmap
│   ├── Boxplot
│   ├── Symbols
│   ├── Protein Domains
│   ├── Color Gradients
│   ├── Shape Plots
│   ├── Text Labels
│   ├── Arrows
│   ├── Connections
│   ├── Tanglegrams
│   ├── Line Charts
│   ├── Images
│   ├── Alignments
│   ├── Phylogenetic Placements
│   ├── Timescales
│   └── Manual Annotations
├── Taxonomy Analysis
│   ├── Auto Ranks
│   ├── Taxonomy Extract
│   ├── Monophyly Check
│   ├── Style Config
│   ├── Binary Conversion
│   └── Connect Pairs
├── API Operations
│   ├── Upload
│   ├── Delete
│   ├── Export
│   └── Status
└── Utilities
    ├── Template Learning
    ├── Tree Info
    ├── Color Tools
    ├── Count to Tree
    └── Column Grouping

Installation

pip install -e .

Dependencies: Python 3.10+, typer, pandas, dendropy, numpy, requests, pydantic, PyYAML, rich, scipy

Quick Verification

pyitol --help
pyitol template create --help
pyitol taxonomy monophyly --help