Data-specific substitution models improve protein-based phylogenetics - data

Amino-acid sequence data sets, estimated data-specific amino-acid substitution models, and optimal ML trees. Data are divided in five folders, each one with a readme.txt file describing it. ├── 1_simulated_data_sets │ ├── 1500-site_alignments │ ├── 400-site_alignments │ └── 8000-site_alignments ├── 2_simulated_data_specific_models │ ├── Codeml_models │ ├── FastMG_models │ ├── IQTREE_models │ ├── P4_BI_models │ └── P4_ML_models ├── 3_optimal_ML_trees_simulated_data │ ├── commonly-used_empirical_models │ │ ├── cpREV_model_analyses │ │ └── WAG_model_analyses │ ├── data_specfic_model_analyses │ │ ├── Codeml-estimated_model_analyses │ │ ├── FastMG-estimated_model_analyses │ │ ├── IQTREE-estimated_model_analyses │ │ ├── P4BI-estimated_model_analyses │ │ └── P4ML-estimated_model_analyses │ └── simulation_model_analyses ├── 4_data_specific_models_empirical_data │ └── Toussaint18_data_specific_models_27partitions └── 5_optimal_ML_trees_empirical_data