MAST: Phylogenetic inference with mixtures across sites and trees (revised)

Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting, introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call MAST. This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show ..., , , # README: MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

[https://doi.org/10.5061/dryad.51c59zwfx(opens in new window)](https://doi.org/10.5061/dryad.51c59zwfx)

Having implemented the MAST model in IQ-TREE, we used simulated data to test the performance of the MAST model under a wide range of scenarios. The first and second simulation experiments test the accuracy of the unlinked and linked MAST models when the true model is specified. The third simulation experiment simulates data with varying levels of introgression to compare the performance of standard (i.e. single-tree) concatenation methods to the performance of the MAST model. The fourth simulation experiment examines the performance of the MAST model when an incorrect model is specified, by applying an unlinked MAST model with different numbers of trees to an alignment simulated under a single tree. 

## Description of the files/folders

Empirical_experiments.tgz : a compressed file containing the data sets,...