Supplementary material of phylogenetic inference with recurrent mutations

Supplementary material The supplementary material is organized into two main folders: case_studies and simulations. 1. **case_studies** The case_studies folder contains all allele count files (.cf) required for the phylogenetic analyses, the RevBayes .rev scripts used for Bayesian phylogenetic inference, and all inference outputs (.log and .tree files). Folder structure: case_studies hcv hcv_subtypes.cf pomo_boundary_hcv.rev pomo_recurrent_hcv.rev output hcv_subtypes_boundary.log hcv_subtypes_boundary.tree hcv_subtypes_recurrent.log hcv_subtypes_recurrent.tree ... hiv hiv_subtypes.cf pomo_boundary_hiv.rev pomo_recurrent_hiv.rev output hiv_subtypes_boundary.log hiv_subtypes_boundary.tree hiv_subtypes_recurrent.log hiv_subtypes_recurrent.tree ... iav H10N7_Avian_boundary.rev H10N7_Avian_recurrent.rev ... data H10N7_Avian.cf H11N9_Avian.cf H13N2_Avian.cf ... output H5N1_Avian_boundary.log H5N1_Avian_recurrent.tree H5N1_Avian_recurrent.trees H5N1_Avian_recurrent.log 2. **simulations** For the sake of space, the rev scripts and the .log and .tree output files for each individual inference are not included. However, the simulations folder contains all the functions needed to simuate the scenarios, the simulated datasets and the master RevBayes scripts used for the Bayesian inferences, allowing the analyses to be fully reproduced. We have also included summary files (those starting with mcmc), which provide the parameter estimates for each scenario. Simulated files follow the naming scheme (or a subset of): t_b_r_f_s_i.txt where t: selection coefficient theta in {1, 0.1, 0.01, 0.001} b: mutation bias in {1, 5} r: root age in {1/10, 1, 10} f: fitness coefficient in {0.5, 0.9, 1, 1.1, 1.5} s: number of sites in {100, 1000, 10000, 100000, 1000000} i: replicate index in {1, ..., 100} For the GTR model, polymorphic states are sampled to fixed states. These files are prefixed with: c_t_b_r_f_s_i.txt Folder structure: simulations phylo_functions.R simulations_selection.R simulations.R simulations_linkage.R simulations_reversed.R simulations_virtual.R simulated_data 1_2_1_3_5_1.txt 1_2_1_3_5_10.txt 1_2_1_3_5_100.txt ... c_1_2_1_3_5_1.txt c_1_2_1_3_5_10.txt c_1_2_1_3_5_100.txt ... scripts_outputs gtr_random.txt mcmc_boundary.txt mcmc_gtr.txt mcmc_recurrent.txt pomo_boundary.txt pomo_recurrent.txt simulated_data_selection 1_2_1_1_4_1.txt 1_2_1_1_4_2.txt 1_2_1_1_4_3.txt ... scripts_outputs_selection mcmc_boundary.txt mcmc_recurrent.txt pomo_boundary.txt pomo_recurrent.txt simulated_data_linkage (cl_t_b_s_i.txt) cl_1_1_1_1.txt cl_1_1_1_2.txt cl_1_1_1_3.txt ... scripts_outputs_linkage mcmc_boundary.txt mcmc_recurrent.txt pomo_boundary.txt pomo_recurrent.txt simulated_data_reversed (bm_t_b_s_i.txt) bm_1_1_1_1.txt bm_1_1_1_2.txt bm_1_1_1_3.txt ... scripts_outputs_reversed mcmc_boundary.txt mcmc_recurrent.txt pomo_boundary.txt pomo_recurrent.txt simulated_data_virtual (t_b_s_i.txt) 1_1_4_1.txt 1_1_4_2.txt 1_1_4_3.txt ... scripts_outputs_virtual mcmc_recurrent.txt pomo_recurrent.txt