mlRho

mlRho estimates population genetic parameters from shotgun sequence data of single diploid individuals using maximum-likelihood inference to infer the population mutation rate (4N(e)μ), sequencing error rate, and population recombination rate (4N(e)c).

Key Features:

• Maximum Likelihood Estimation: Employs maximum likelihood estimators to infer evolutionary parameters from sequence data.
• Population Mutation Rate (4N(e)μ): Calculates the population mutation rate (4N(e)μ) from shotgun sequence data of single diploid individuals.
• Sequencing Error Rate: Estimates sequencing error rates alongside genetic parameters to separate true variation from technical error.
• Population Recombination Rate (4N(e)c): Computes the population recombination rate (4N(e)c) to assess recombination dynamics.

Scientific Applications:

• Ecological and Evolutionary Studies: Quantifies genetic diversity, mutation rates, and recombination dynamics for ecological and evolutionary inference.
• Comparative Genomics: Applied to compare genomes of species with contrasting reproductive strategies, exemplified by Ciona intestinalis and Daphnia pulex.

Methodology:

Extends theoretical frameworks to process shotgun sequence data from single diploid individuals using maximum likelihood estimators, with parameter estimates validated on simulated datasets.