The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

Empirical trees used in the study are trees from the literature, collected by TimeTree (timetree.org). Run ```Tree_Selection.R``` to select the empirical phylogenetic trees to be included from TimeTree. The output file ```final_timetrees.RData``` contains the final subset of empirical phylogenetic TimeTree trees used for analysis with anonymized tip labels. 2. Run ```Simulation_And_Analysis.R``` to fit birth and death parameters (assuming rho = 1) for each of the 1189 empirical trees, simulate 1000 trees per empirical tree, calculate tree index values for both empirical and simulated trees, and calculate z-scores comparing the simulated and empirical trees. Note that calculating the tree index values for the simulated trees is VERY time-consuming due to the number of trees. Run ```Supplementary_Fig_S1_Analysis.R``` to generate data for Supplementary Figure S1. 3. Run ```Meta_analysis.R``` to run the linear regression models to investigate the role of the prior/analysis type for the subset (n=300) of the included empirical trees. The metadata for the 300 trees can be found in the supplementary files (Table S3). 4. Run ```Imbalance_Simulation.R``` to run the simulations for the imbalanced data subset (100 trees). Simulated sequences for each tree were run through RevBayes and IQ-TREE 2, as mentioned previously. Note: To avoid later confusion, the three various substitution rates used (0.5, 0.05, 0.005) are referred to as Rates 2-4 in the code. There is therefore no Rate 1; apologies in advance for any confusion. The shell scripts to run the inferences in each software are as follows: 4a. RevBayes: ```fasta_to_revbayes_code_rate2.sh```, ```fasta_to_revbayes_code_rate3.sh```, ```fasta_to_revbayes_code_rate4.sh``` These shell scripts use the following .Rev files: ```MCMC_Revbayes_code_rate2.Rev```, ```MCMC_Revbayes_code_rate3.Rev```, ```MCMC_Revbayes_code_rate4.Rev``` And rely on the following supplementary .Rev files: ```tree_BD.Rev```, ```sub_JC.Rev```, ```clock_global.Rev``` 4b. IQ-TREE 2: ```fasta_to_iqtree_code.sh``` 5. Run ```Final_Figures.R``` to visualize the results.