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Related Experiment Video

Updated: Dec 15, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler.

Connor Morgan-Lang¹, Ryan McLaughlin¹, Zachary Armstrong²

¹Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.

Bioinformatics (Oxford, England)

|July 9, 2020

Summary

TreeSAPP software accurately classifies microbial genes and pathways, improving understanding of global biogeochemical cycles. This tool enhances taxonomic assignment for environmental genomes, addressing gaps in sequence databases.

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Area of Science:

Microbiology
Bioinformatics
Computational Biology

Background:

Microbial communities are crucial for global biogeochemical cycles.
Many key microbial taxa are underrepresented in sequence databases, leading to inaccurate genomic analysis.
Accurate functional and taxonomic classification of microbial genes is essential for understanding ecosystem processes.

Purpose of the Study:

To develop and present Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software.
To improve the functional and taxonomic classification of genes, reactions, and pathways from microbial genomes.
To address the limitations of current methods in assigning sequences from underrepresented microbial groups.

Main Methods:

TreeSAPP utilizes a reference package of coding sequences involved in biogeochemical cycles.
The software employs linear regression of evolutionary distance on taxonomic rank for enhanced classification accuracy.
It can classify both assembled and unassembled sequences, supporting interactive visualizations.

Main Results:

TreeSAPP provides accurate functional and taxonomic classifications for microbial genes and pathways.
The software effectively assigns both closely related and divergent sequences to their appropriate taxonomic ranks.
It offers quantitative classifications and supports interactive tree of life visualizations.

Conclusions:

TreeSAPP significantly improves the accuracy of taxonomic and functional gene assignment in microbial genomics.
The software enhances the study of microbial roles in global biogeochemical cycles by leveraging underrepresented data.
TreeSAPP is a valuable open-source tool for researchers analyzing environmental microbial genomes.