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