COMPASS

COMPASS simulates sequence evolution across arbitrary discrete state spaces along phylogenetic trees to generate simulated sequence alignments for testing and validating sequence analysis methods using time-reversible models.

Key Features:

• Arbitrary discrete state spaces: Simulates evolutionary processes on any user-specified discrete state space rather than being limited to fixed alphabets.
• Phylogenetic tree-based simulation: Evolves sequences along input phylogenetic trees to produce alignment data consistent with tree topology.
• Time-reversible models: Supports simulation under time-reversible substitution models.
• Simulated sequence alignments: Produces multi-sequence alignments suitable for downstream method testing and benchmarking.
• Customizable sequence data: Enables generation of sequence data that can mimic a wide array of biological scenarios for validation and exploration.
• Implementation: Implemented in Python 2.7.

Scientific Applications:

• Method testing and validation: Generates controlled datasets for testing and validating sequence analysis and phylogenetic inference tools.
• Theoretical model exploration: Allows exploration and comparison of theoretical models of sequence evolution on nonstandard state spaces.
• Simulation of evolutionary scenarios: Produces data that can mimic real-world evolutionary patterns for method assessment.

Methodology:

Simulations are performed along phylogenetic trees under time-reversible substitution models on arbitrary discrete state spaces; the software is implemented in Python 2.7.