SimPhy

SimPhy simulates the evolution of multiple gene families under incomplete lineage sorting (ILS), gene duplication and loss (GDL), horizontal gene transfer (HGT), and gene conversion to study gene–species tree discordance.

Key Features:

• Hierarchical phylogenetic model: Implements a hierarchical model that simulates species, locus, and gene trees governed by global and local parameters.
• Parameter flexibility: Supports genome-wide, species-specific, and locus-specific parameters that can be fixed or sampled from predefined statistical distributions.
• Modeled evolutionary processes: Explicitly models incomplete lineage sorting (ILS), gene duplication and loss (GDL), horizontal gene transfer (HGT), and gene conversion.
• Substitution rate variation: Models substitution rate variation among lineages using uncorrelated relaxed clocks.
• Sequence alignment generation: Generates partitioned nucleotide, codon, and protein multilocus sequence alignments under diverse substitution models via integration with INDELible.
• Validation and performance: Validated against theoretical expectations and compared with other programs such as DLCoal-Sim, showing faster performance and scalability on complex models and large trees.

Scientific Applications:

• Gene-family evolution and discordance: Simulating gene-family evolution to study causes and patterns of gene–species tree discordance.
• Process interaction studies: Investigating interactions among ILS, GDL, HGT, and gene conversion and their joint effects on phylogenetic inference.
• Method benchmarking and bias assessment: Assessing systematic biases in reconciliation and inference methods, for example the overestimation of duplication times by standard reconciliation approaches.

Methodology:

Uses a hierarchical phylogenetic model to simulate species, locus, and gene trees with parameters either fixed or sampled from predefined statistical distributions, applies uncorrelated relaxed clocks for substitution rate variation, and generates partitioned nucleotide, codon, and protein multilocus alignments via INDELible.