PAML

PAML performs maximum-likelihood phylogenetic analyses of DNA and protein sequences to estimate evolutionary parameters and test evolutionary hypotheses.

Key Features:

• Estimation of Synonymous and Nonsynonymous Rates: Calculates synonymous (d(S)) and nonsynonymous (d(N)) substitution rates between protein-coding DNA sequences.
• Inference of Positive Darwinian Selection: Infers positive selection by conducting phylogenetic comparisons of protein-coding genes using maximum-likelihood approaches.
• Reconstruction of Ancestral Sequences: Reconstructs ancestral genes and proteins for downstream molecular and evolutionary analyses.
• Analysis of Heterogeneous Data Sets: Facilitates combined analyses of diverse data sets from multiple gene loci.
• Estimation of Species Divergence Times: Estimates species divergence times while incorporating uncertainties in fossil calibrations.
• Evolutionary Models: Implements an extensive array of evolutionary models to estimate parameters related to sequence evolution and enable hypothesis testing.
• Phylogenetic Tree Comparison and Testing: Compares and tests phylogenetic trees using maximum-likelihood methods.

Scientific Applications:

• Phylogenetic inference and model comparison: Derives and compares phylogenetic trees under different evolutionary models to evaluate tree topologies and model fit.
• Detection of adaptive evolution: Identifies genes or sites under positive Darwinian selection in protein-coding sequences.
• Evolutionary rate analysis: Quantifies d(S) and d(N) to assess selective pressures on genes.
• Ancestral sequence reconstruction for molecular palaeobiology: Reconstructs ancestral proteins and genes to support molecular restoration and evolutionary functional inference.
• Multi-locus phylogenetics: Integrates data from multiple gene loci for combined phylogenetic analyses.
• Divergence time estimation: Provides a temporal framework for evolutionary events by estimating species divergence times with fossil calibration uncertainty.

Methodology:

Uses maximum-likelihood estimation under multiple evolutionary models; performs phylogenetic comparisons and likelihood-based hypothesis testing; reconstructs ancestral sequences by maximum likelihood; estimates divergence times incorporating uncertainties in fossil calibrations.