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Area of Science:

  • Evolutionary biology
  • Bioinformatics

Background:

  • Phylostratigraphy aims to determine the evolutionary origin of genes within a species.
  • This involves identifying homologous genes across progressively wider taxonomic groups (clades).

Purpose of the Study:

  • To introduce phylostratr, a comprehensive R-based framework for automating phylostratigraphy analysis.
  • To enable accurate estimation of phylostrata for all genes in a given species.

Main Methods:

  • The phylostratr framework automates species selection, sequence retrieval, database construction, and phylostratum inference.
  • It incorporates key diagnostics for assessing results, including homolog detection, proteome quality, and potential errors.
  • The package offers extensive customization options for clade trees, sequence sources, homology detection algorithms, and classification sensitivity.

Main Results:

  • phylostratr successfully automates the complex process of phylostratigraphy.
  • The framework provides valuable diagnostics to ensure the reliability of inferred phylostrata.
  • Case studies in Arabidopsis thaliana and Saccharomyces cerevisiae demonstrate the utility of phylostratr.

Conclusions:

  • phylostratr is a versatile and powerful tool for phylostratigraphy.
  • It facilitates systematic comparisons and enhances the accuracy of evolutionary origin inference for genes.