The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree...

Area of Science:

• Computational Biology
• Phylogenetics
• Bioinformatics

Background:

• Supertrees are crucial for macroevolutionary studies, comparative biology, and biodiversity research.
• Creating large supertrees (thousands to tens of thousands of taxa) requires processing numerous individual phylogenies.
• Existing software solutions lack ease of use and full integration for large-scale supertree construction.

Purpose of the Study:

• To present a new, user-friendly Python-based software package for building large supertrees.
• To address the limitations of current software in managing and processing extensive phylogenetic data.
• To facilitate macroevolutionary and biodiversity research by simplifying supertree creation.

Main Methods:

• Development of a Python software package utilizing a well-defined XML schema for data and metadata management.
• Integration of new processing steps, including Safe Taxonomic Reduction.
• Implementation of a user-friendly graphical user interface (GUI) and a command-line tool for data manipulation via a flexible processing pipeline.

Main Results:

• The software successfully stores and processes data from over 1000 trees for supertree analyses.
• The package integrates tree and metadata into a single file using a revised storage format.
• Processing steps include name standardization, taxon management, taxonomic overlap assessment, data independence, and safe taxonomic reduction.

Conclusions:

• The new software significantly simplifies the creation of large supertrees.
• It offers enhanced flexibility for data manipulation and further research in phylogenetics and evolutionary biology.
• This tool makes complex phylogenetic analyses more accessible to researchers in various biological fields.