OneTwoTree: An online tool for phylogeny reconstruction

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Phylogeny reconstruction is crucial for understanding evolutionary relationships, ecology, conservation, and systems biology.
• The growing volume of genomic data necessitates efficient computational tools for accurate and high-resolution phylogenetic analyses.
• Manual processing of large sequence datasets is time-consuming and prone to errors.

Purpose of the Study:

• To introduce OneTwoTree, a novel web-based tool for automated phylogeny reconstruction using the supermatrix approach.
• To provide researchers with an efficient and user-friendly platform for species-tree reconstruction.
• To facilitate the utilization of extensive genomic data for phylogenetic analyses.

Main Methods:

• OneTwoTree retrieves sequence data from NCBI GenBank based on user-provided taxa names.
• The tool clusters sequences into orthology groups, identifies informative markers, and selects an outgroup.
• It assembles a partitioned sequence matrix for phylogeny reconstruction, with options for user-defined parameters.

Main Results:

• OneTwoTree demonstrated superior performance compared to manual reconstruction, achieving higher data coverage in taxon sampling.
• The tool significantly increased the number of informative markers assembled for phylogenetic analysis.
• User control over merging similar clusters and selecting genome types enhances flexibility.

Conclusions:

• OneTwoTree offers a flexible and efficient online solution for species-tree reconstruction.
• The tool assists researchers of all expertise levels in navigating complex genomic data for phylogenetic analysis.
• It streamlines the process, improving data coverage and marker selection for more robust evolutionary insights.