Version 0.1.0

Version 0.1.0

Initial Release

This initial release establishes the foundation of the Molecular Clock project with the implementation of a strict molecular clock simulation framework.

The simulator generates complete synthetic evolutionary datasets from first principles, providing a known evolutionary history that can be used to develop and validate future molecular clock algorithms.

Features

• Generate random ancestral DNA sequences.
• Construct rooted binary phylogenetic tree topologies.
• Calibrate trees under a strict molecular clock to produce ultrametric trees.
• Simulate DNA sequence evolution along each branch.
• Record the complete evolutionary history, including internal nodes and mutation events.
• Export simulated datasets in FASTA, Newick and JSON formats.
• Configuration-driven simulations using JSON configuration files.
• Fully reproducible simulations through configurable random seeds.

Documentation

This release includes initial project documentation covering:

• Simulation architecture
• Workflow and design
• Configuration reference
• Simulator operation

Looking Ahead

The strict molecular clock simulator provides the “forward model” for the project—simulating sequence evolution from a known evolutionary history.

Future releases will focus on the inverse problem: reconstructing phylogenetic relationships and estimating divergence times from simulated sequence data through the implementation of molecular clock inference algorithms.