queeems

queeems quantifies the extent of evolutionary evidence retained in molecular sequences using a Bayesian approach to assess sequence saturation and generate site-specific Bayes factors with respect to codon bases.

Key Features:

• Bayesian Saturation Assessment: Evaluates whether evolutionary information in genetic sequences has eroded over time through a Bayesian function rather than ad hoc hypothesis tests.
• Site-Specific Bayes Factors: Generates Bayes factors at individual sites relative to codon bases for downstream computational analyses.

Scientific Applications:

• Natural Selection Analyses: Provides site-specific evolutionary evidence metrics that enable straightforward integration into extensive computational biology inquiries including natural selection studies.
• Phylogeny Quality Control: Determines whether genetic sequences retain sufficient evolutionary signatures to support reliable biological inferences and phylogeny reconstruction.

Methodology:

The method employs a Bayesian function to assess sequence saturation, generating site-specific Bayes factors with respect to codon bases.