This repository contains some of the materials used for the manuscript "GTRpmix: A linked general-time reversible model for profile mixture models"

1. The nexus file Matrices_GTR20.nex contains in nexus format the matrices EAL, ELM, ELM50, MXM, MXMfix, and FM described in the main manuscript.

2. The folder trees contain the Newick format for trees depicted in the Supplementary material Figures S1, S10, and S11 (denoted Sim1.treefile, ELM.treefile, and EAL.treefile) and another tree ELM_50tax.treefile. The tree 'Sim1.treefile' was used to generate the simulations described in the section 'Parameter Estimation Performance' of the main manuscript. The trees ELM.treefile, ELM_50tax.treefile, and EAL.treefile were used to create the matrices ELM, ELM50, and ELM, respectively, as described in the main manuscript.

3. The folder Dataset contains two subdirectories, the subdirectory ELM contains the Pan-Eukaryotic data sets described in the section 'Data Sets' of the paper. The dataset denoted EAL_data.fas is the 78-taxon dataset while ELM50_data.fas is the 50-taxon dataset. Additionally, the files ELM.indices.tsv and ELM50.indices.tsv contain the partition file for every protein for the datasets ELM and ELM50 respectively. The subdirectory EAL contains the Eukaryotic-Archaeal data set, denoted EAL_data.fas, described in the section 'Data Sets' of the paper. Additionally, the file EAL_partition.out contains the partition file for every protein for such dataset.