IQ2MC

IQ2MC integrates IQ-TREE 3 and MCMCTree for phylogenetic time tree inference, enabling the use of complex substitution models and significantly speeding up the pre-calculation steps for estimating divergence times.

Key Features:

• IQ-TREE 3 Integration: IQ2MC provides an updated version IQ-TREE 3.0.1 to calculate the gradients and Hessian at the maximum likelihood branch lengths.
• MCMCTree Integration: MCMCTree is used for MCMC sampling of divergence times following the pre-calculation steps.
• Complex Model Support: IQ2MC allows the use of a wide range of IQ-TREE's complex models in divergence time inference, including several advanced partition models and mixture models not available in the current MCMCTree workflow.
• Pre-calculation Speedup: The framework substantially speeds up the pre-calculation steps required for MCMCTree's fast approximate likelihood calculation.

Scientific Applications:

• Divergence Time Estimation: IQ2MC enables reliable estimates of divergence times in deep phylogenies by supporting complex substitution models required for accurate dating.
• Phylogenetic Time Tree Inference: The framework facilitates seamless workflow for estimating divergence times with greater accuracy using integrated maximum likelihood and Bayesian approaches.
• Empirical Dataset Analysis: IQ2MC has been applied to simulated and empirical datasets of placental mammals, plants, eukaryotes/prokaryotes, and metazoan.

Methodology:

IQ2MC calculates the gradients and Hessian at the maximum likelihood branch lengths using IQ-TREE 3.0.1, then uses MCMCTree for MCMC sampling of divergence times. The framework implements fast approximate Markov Chain Monte Carlo sampling for times along a fixed tree topology.