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Updated: Apr 16, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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BMX: a tool for computing bacterial phyletic composition from orthologous maps.

Benard W Kulohoma

    BMC Research Notes
    |March 11, 2015
    PubMed
    Summary

    Bacterial Makeup eXplorer (BMX) is a new tool for analyzing bacterial genomes. It efficiently determines orthologs, enabling high-resolution comparison of diverse bacterial populations and understanding evolutionary relationships.

    Area of Science:

    • Microbiology
    • Genomics
    • Bioinformatics

    Background:

    • Advancements in sequencing technologies enable higher-resolution exploration of microbial genetic diversity.
    • Comparing bacterial genomes and understanding evolutionary relationships from large datasets remains challenging.
    • Existing clustering algorithms require new tools for analyzing orthologous maps and gene presence/absence patterns.

    Purpose of the Study:

    • To develop a novel algorithm for efficient ortholog determination in prokaryotic genomes.
    • To enable robust, scalable, and high-quality annotation transfer across diverse bacterial genomes.
    • To facilitate gene-by-gene composition assessment and analysis of phyletic patterns.

    Main Methods:

    • Implementation of the Bacterial Makeup eXplorer (BMX) algorithm.

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  • Reference-free approach for determining orthologs in prokaryotic genomes.
  • Integration of orthologous maps from highly diverse prokaryotic genomes.

    • Main Results:

    • BMX swiftly and efficiently determines the number of orthologs, facilitating annotation transfer.
    • The tool integrates orthologous maps from diverse genomes for robust analysis.
    • Results are presented in publication-quality figures, aiding in composition assessment.

    Conclusions:

    • BMX enables extensive analysis of orthologous maps to understand biological relationships.
    • The software is portable across platforms and easy to install.
    • BMX facilitates higher-resolution analysis of genomes from diverse bacterial populations.