Rabies Mutation

Creator: Rowan Durrant - School of Biodiversity, One Health & Veterinary Medicine, Glasgow University

Contact me: r.durrant.1@research.ac.uk

Description: Repo for code and data used in the manuscipt "Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus".

Input

• EF_simulations - output from a branching process simulation which we simulate mutations onto.
• Pemba_assigment.csv - Lineages of each sequence in the Pemba dataset from Lushasi et al., 2023, assigned using MADDOG.
• pemba non timescaled.txt - TempEst divergence time plot output for Pemba data
• pemba_m6_m7.txt - log file from Lushasi et al.'s BEAST run
• pemba_tz_n153.aln.fasta - Pemba sequences
• pemba_tz_n153_timescaled.mcc.tre - Pemba timescaled tree
• serial_interval_clean_RD.csv - raw serial interval estimates from Mancy et al., 2022

Code: How does rabies mutate? - Figure 2

• 2b_simulate_perfect_clockrate.R takes simulation output and generates mutations onto cases using a clock rate model (mutations accumulate per unit time). Uses mutations_function_time.R.
• 2a_simulate_per_generation.R does the same, but with a per-generation mutation model. Uses mutations_function.R.
• 3_compare_clockrate_gen_divergence.R makes divergence-time plots and compares R^2 values for both per-time and per-generation simulations.
• 7_nice_graphs.R - makes graphs

Code: What is RABV's mutation rate?

Simulations to test accuracy - Figure 3

• 1_sim_output_prep.R - takes simulation output and generates mutations onto cases using a clock rate model (mutations accumulate per unit time). Uses mutations_function.R.
• 2a_simulate_per_generation.R as above
• 4_clock_method_accuracy.R - calculates the SNP/gen prediction method's accuracy.
• 7_nice_graphs.R - makes graphs

Applications to Pemba dataset - Figure 4

• 5_clock_rate_method_bayesian_combine_uncertainties.R - calculate SNPs/gen
• 6_clock_rate_method_pemba_distribution.R - fits distribution to output.
• 7_nice_graphs.R - makes graphs
• 8_no_gens_before_SNPs.R - simulates how many generations occur before a substitution happens

Output

• simulation - folder with output files relating to all the simulated methods, including divergence-time plot related data and mutation rate calculation method accuracy.
• pemba - folder with output files relating to calculating the per-generation substitution rate from real RABV sequences.

Plots

Files of plots used in the manuscript.