Contents:

• TreeProfiler Tutorial
• Introduction
• Table of Contents
• Installation
  • Quick install via pip
  • Quick Start with examples dataset
  • Manual installation
  • Dependencies
    • Install ETE v4
    • Install TreeProfiler
  • Input files
  • Basic Usage
• Using TreeProfiler
  • Reading input tree
    • Tree format
    • Tree parser
  • treeprofiler-annotate computing phylogenetic profiles and annotation
    • Annotate metadata into tree
    • Taxonomic annotation
    • Functional annotation
    • Analytical methods in treeProfiler
    • Output formats for annotated trees
  • treeprofiler-plot visualizing phylogenetic profiles and annotation
    • Interactive visualization interface
    • Basic options of visualizing layouts
    • Layouts for categorical data
    • Layouts for boolean data
    • Layouts for Numerical data
    • Layouts for Analytical Data
    • Layouts for Multiple Sequence Alignment
    • Layouts for eggnog-mapper pfam/smart annotations
    • Layouts for eggnog-mapper functional annotations
    • Layouts for Taxonomy annotation
    • Customize color in layout with color config
  • Conditional query in annotated tree (can be used in both annotate and plot)
    • Query Syntax
    • Conditional limit based on taxonomic level
    • Choose the metric for internal nodes in numerical layout
  • Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3
  • Demo2 Explore large NifH gene tree with functional and taxonomic information