DOI: 10.5281/zenodo.17648648
title: Supplementary material of phylogenetic inference with recurrent mutations

description: 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:

 

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

 

    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