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Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry
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TreeProfiler: large-scale metadata profiling along gene and species trees.

Ziqi Deng1, Claudia Sanchis-López1, Ana Hernández-Plaza1

  • 1Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid 28223, Spain.

Molecular Biology and Evolution
|February 1, 2026
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Summary

TreeProfiler automates the analysis of biological traits on gene and species trees. This tool efficiently handles large datasets for comparative genomics and evolutionary studies.

Keywords:
phylogenetic profilingphylogeneticstree annotationtree visualization

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Area of Science:

  • Comparative genomics
  • Bioinformatics
  • Evolutionary biology

Background:

  • Phylogenetic profiling is crucial for inferring gene function, ancestral states, and ecological associations.
  • Existing tools lack scalability and robust methods for summarizing traits at internal tree nodes.

Purpose of the Study:

  • Introduce TreeProfiler, a novel tool for automated annotation and exploration of biological traits on large phylogenetic trees.
  • Address limitations of existing profiling tools regarding scalability and trait summarization.

Main Methods:

  • TreeProfiler supports profiling of custom continuous and discrete traits.
  • Incorporates ancestral character reconstruction and phylogenetic signal tests.
  • Integrates genomic features like sequence alignments, protein domains, and functional annotations.

Main Results:

  • Demonstrated efficient handling of massive datasets, including over 400,000 sequences for the methyl-accepting chemotaxis protein family.
  • Successfully profiled the relative abundance of nearly 125,000 species across 51 biomes.
  • Showcased TreeProfiler's utility beyond traditional phylogenetic profiling.

Conclusions:

  • TreeProfiler provides a scalable and versatile solution for analyzing biological traits on phylogenetic trees.
  • Facilitates automated annotation and interactive exploration of complex genomic and ecological data.
  • Offers advanced features for comparative genomics and evolutionary research.