Free Rate Model

Package for BEAST 2.

This package contains the free rate model allowing site model heterogeneity where the

When to Use the Free Rate Model

• When there is strong evidence of rate heterogeneity across sites.
• When the dataset is large enough to support the estimation of many rate parameters.
• When the biological question requires a detailed understanding of site-specific evolutionary rates.

Limitations

• Overfitting: With too many parameters, the model may overfit the data, especially with small datasets.
• Computational Demand: The model can be slow to estimate, especially for large alignments.

Installation

The latest version is for BEAST v2.7, which can be obtained from here.

• In BEAUti, select File/Manage packages
• Select FreeRateModel from the list
• Click the Install button

Usage

• In BEAUti, select the Site model panel
• Select Free Rate Model from the drop-down list

References

Soubrier J, Steel M, Lee MS, Der Sarkissian C, Guindon S, Ho SY, Cooper A. The influence of rate heterogeneity among sites on the time dependence of molecular rates. Molecular biology and evolution. 2012 Nov 1;29(11):3345-58. https://doi.org/10.1093/molbev/mss140

Le SQ, Dang CC, Gascuel O. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Molecular biology and evolution. 2012 Oct 1;29(10):2921-36. https://academic.oup.com/mbe/article/29/10/2921/1027701