Version 0.4.0

Relaxed Molecular Clock Explorer

This release introduces the Relaxed Molecular Clock Explorer, providing an interactive environment for exploring sequence evolution under a simple relaxed molecular clock model.

Built directly on top of the Relaxed Molecular Clock Engine introduced in v0.3.0, the explorer allows lineage-specific mutation rates to be adjusted interactively before generating and visualising complete simulated evolutionary histories.

This release brings the relaxed clock implementation to feature parity with the existing strict clock workflow, combining command-line dataset generation with an interactive visualisation environment.

Highlights

• Added the Relaxed Molecular Clock Explorer
• Interactive adjustment of relaxed clock simulation parameters
• Visualisation of lineage-specific mutation rates and accumulated genetic change
• Simulation summary including mutation rate statistics and expected substitutions
• Support for exporting FASTA, Newick and JSON outputs directly from the explorer
• New workflow documentation describing the relaxed clock simulation pipeline
• Comprehensive Wiki documentation for the Relaxed Molecular Clock Engine and Explorer
• Updated project documentation to include both strict and relaxed molecular clock workflows

Overview

The Relaxed Molecular Clock Explorer provides an intuitive way to investigate how variation in mutation rates influences molecular evolution.

Users can interactively adjust:

• Tree structure and branch durations
• Sequence length
• Root mutation rate
• Rate variation (sigma)
• Minimum and maximum lineage rates
• Mutation behaviour
• Random seed

Each simulation produces a complete synthetic evolutionary history together with an interactive phylogenetic tree, simulation summary statistics and downloadable outputs.

Project Status

The project now includes two complementary molecular clock implementations:

• Strict Molecular Clock – constant evolutionary rate across all lineages.
• Relaxed Molecular Clock – lineage-specific mutation rates using a simple autocorrelated model.

Both implementations provide:

• Independent simulation engines
• Command-line interfaces
• Interactive Streamlit explorers
• FASTA, Newick and JSON exports
• Comprehensive documentation

Together these provide a foundation for investigating how different molecular clock assumptions influence simulated evolutionary histories.

Looking Ahead

With both strict and relaxed molecular clock models now supported through command-line tools and interactive explorers, the next stage of the project will shift from simulation to phylogenetic reconstruction.