Relative model fit does not predict topological accuracy in single-gene protein phylogenetics

Please direct all questions or comments to Stephanie via spielman <AT> rowan <DOT> edu.

Contents

• All directories and SLURM scripts are named as one of the following, representing the data they process:

  • simulation: MutSel simulations
  • simulation_control: WAG+I+G simulations
  • pandit: PANDIT analysis

• scripts/ contains all code for generating data, results, including SLURM (*sbatch) submission scripts for HPC

• simulations/ contains all simulated alignments, DMS preferences, and phylogenies used for simulation. Simulations were performed with scripts/simulate.py and scripts/simulate_control.py and associated scripts/submit_simulations.sbatch (for MutSel only, as those are slower than WAG which are quickly run locally).

• selected_models_* contains all results from model selection using ModelFinder with option -m TESTONLY. Contents created with scripts/submit_model_selection_*.sbatch

• processed_model_selection/ contains CSV's of results from model selection, including scores for all models as well as the specific "quantile" models. Contents created with with scripts/process_model_selection.sh (calls scripts/selected_models_to_csv.py and scripts/parse_selected_models.R)

• fitted_trees_ufb_* contains all inferred phylogenies with IQTREE and various associated logfiles. Contents created with scripts/infer_trees.py and associated scripts/submit_tree_inference_*.sbatch.

• topology_tests_* contains results from AU tests as produced by IQTREE. Contents created with scripts/run_topology_tests.py.

• results_analysis/ contains a post-processing R script for stats+viz, relevant CSV files to post-process, and directory of figures used in MS produced by said script.

  • csv_files/ contains all processed CSVs created with one of the scripts in scripts/
    • all_models_pearson.csv contain Pearson correlations among rate matrices (exchangabilities only!), created by scripts/compare_all_models.py
    • rf_fit_*.csv contains robinson-foulds distances from true tree, and BIC, for all simulations. Contents created with scripts/calculate_rf_ufb.py.
    • rf_pandit.csv contains all-to-all RF distances for PANDIT data. Contents created with scripts/calculate_rf_ufb.py.
    • topology_tests_*.csv contains summarized results for topology tests. Contents created with scripts/parse_topology_tests.py
  • load.R loads up data, libraries, and formats data for analysis in:
    • build_main_figures.R creates all manuscript figures, saved in main_figures/
    • build_si_figures_tables.R creates all SI manuscript figures and exports CSV tables, saved in si_figures_tables/
    • linear_model_and_misc_wrangling.Rmd performs all linear models presented in the manuscript, and some miscellaneous data wrangling.