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MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Maxwell Sanderford1, Sudip Sharma1,2, Glen Stecher1

  • 1Institute for Genomics and Evolutionary Medicine, Temple University, 1925 N. 12th Street, Philadelphia, PA 19122, USA.

Molecular Biology and Evolution
|September 19, 2025
PubMed
Summary
This summary is machine-generated.

Evolutionary sparse learning, a machine learning approach, builds evolutionary models using genomic data. The MyESL software provides efficient, open-source tools for these analyses, aiding in phylogenomic applications.

Keywords:
machine learningmolecular evolutionphylogenomicssparse learning

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Area of Science:

  • Computational Biology
  • Evolutionary Genetics
  • Bioinformatics

Background:

  • Evolutionary sparse learning integrates machine learning with phylogenetic analysis.
  • Genomic sites are treated as parameters in evolutionary models.
  • Existing tools lack specialized, efficient methods for evolutionary sparse learning.

Purpose of the Study:

  • To introduce MyESL, an open-source software for evolutionary sparse learning.
  • To provide efficient tools for phylogenomic data preprocessing and model analysis.
  • To facilitate the application of evolutionary sparse learning in biological research.

Main Methods:

  • Utilizes Least Absolute Shrinkage and Selection Operator (LASSO) with bi-level sparsity.
  • Implements core logistic regression models in C++ for efficiency.
  • Develops Python-based tools for data preprocessing and result post-processing.

Main Results:

  • MyESL offers computationally efficient evolutionary sparse learning.
  • The software provides evolution-friendly input/output formats.
  • Demonstrated utility in identifying outlier sequences, fragile clades, and modeling convergent traits.

Conclusions:

  • MyESL enhances the application of evolutionary sparse learning in phylogenomics.
  • The software's efficiency and accessibility promote broader use.
  • Open-source availability facilitates integration and further development.