SiteSampler

SiteSampler samples sites from sequence alignments to generate replicate datasets for analyzing substitution-rate variation across lineages and sites in metazoan mitochondrial genomes for phylogenetic and molecular-dating studies.

Key Features:

• Site sampling: Samples individual nucleotide sites from sequence alignments to produce replicate datasets for downstream analyses.
• Replicate dataset generation: Creates multiple resampled alignment replicates to assess the impact of site-level variation on inferred parameters.
• Partitioned relaxed-clock support: Facilitates application of partitioned relaxed-clock models by enabling separate treatment of codon positions of protein-coding genes.
• Java implementation: Implemented in Java for cross-platform execution within bioinformatics workflows.

Scientific Applications:

• Molecular phylogenetics: Evaluates how site-specific variation influences phylogenetic inference from metazoan mitochondrial genomes.
• Molecular dating: Supports dating analyses that account for lineage- and site-specific substitution-rate heterogeneity.
• Model comparison: Enables comparison of clock models (e.g., strict-clock vs. relaxed-clock) using statistical measures such as Bayes factors.
• Rate heterogeneity analysis: Assesses variation in substitution rates among lineages and across codon positions, including applications to cetacean mitogenomes.

Methodology:

Samples sites from sequence alignments to generate replicate datasets and to enable application of partitioned relaxed-clock models, including fitting separate relaxed-clock models to different codon positions; supports subsequent model comparison using Bayes factors.