This repository contains notes on replicating results from Weber and Whelan, 2019 (https://doi.org/10.1093/molbev/msz003) using BppSuite (https://github.com/BioPP/bppsuite; Guéguen et al., 2013).
The folder ./scripts/run_models/ contains configuration information and scripts.
The CoRa model is specified by setting the model parameter to CodonAAClustFreq(model=K80(),frequencies=F3X4). Other equilibrium frequency settings may also be used.
Custom amino acid partitions can also be specified. By default partition=(1,2,3,3,3,2,2,1,2,4,4,2,4,4,1,3,3,2,2,1)will be used. The order of the amino acids in the list is ARNDCQEGHILKMFPSTWYV, and the partitions indicate small non-polar, large polar, small polar, and large non-polar amino acids.
The configuration files provided in this repository were tested with Bio++ v 2.4.0, and you will need to check out this commit of bpp-phyl in order to use the model. The structure of the configuration file has changed in more recent versions. See here for an example of how to set up M0 if you wish to use a newer version of Bio++. However, please be aware that I have not formally benchmarked this setup.
Alignments from large-Ne taxa (blue) disfavour radical nonsynonymous substitutions, while small-Ne taxa (red) show a less pronounced pattern for both comparisons.
Statistical support for CoRa over M0, as indicated by values falling above the vertical black line, is consistently stronger when Ne is large.
Minor discrepancies in estimates may be driven by slight differences in optimisation, gap handling, lower bounds on parameter estimates and starting trees.
Weber CC and Whelan S (2019) Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations. Molecular Biology and Evolution. 36 (4), pp. 679–690 https://doi.org/10.1093/molbev/msz003
Guéguen L. et al. (2013) Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution. Molecular Biology and Evolution. 30 (8), pp. 1745–1750 https://doi.org/10.1093/molbev/mst097
ModeloMatic's model selection function is now available in IQ-Tree: (http://www.iqtree.org/)