PoW_model

Ghafari et al.: A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses

Codes

Evolve_sequences.nb: Generates simulated sequences under the Wright-Fisher model based on a neutral and/or compensatory evolution. Output files are (1) initial_sample.txt (first snapshot from the population after 10N_e generations) (2) final_sample.txt (final snapshot from the population after 10N_e + T generations where T is the time window of rate measurement)

neutral.nb: Extracts and plots the inferred root heights and clock rates from BEAST log file for the purely neutral scenario, i.e. no epistatic sites.

epistatic.nb: Extracts and plots the inferred root heights and clock rates from BEAST log file for the epistatic scenario.

PoW_ultrametric.R: This is the code to generate PoW-transformed trees from the maximum clade credibility distance trees for FV, HCV, and sarbecovirus datasets.

stats folder includes the log files for parameter inference, along with the inferred mean and median clock rates using BEAST. The files in this folder are named in the following format: *_mA_B letter A varies from 2 to 5 and corresponds to substitution rates ranging from 3x10^-2 to 3x10^-5 and letter B takes the values corresponding to the time window of observation, i.e. T=10, 100, 1000, 10000, 100000, 1000000, 10000000

Outputs

*_&_%_PoWtransformed.trees: Contains the PoW-transformed trees (produced by PoW_model_fixedRate.R or PoW_model_variedRate) for * = FV, HCV, and sarbecovirus datasets using & = JC69 or HKY85 substitution models. This includes % = fixedRate or variedRate whereby the short-term rate and fastest-evolving rate groups are either fixed or varied.

*.log: Contains output log files produced by BEAST for * = HCV and sarbecovirus heterochronous datasets (i.e., standard substitution models used to infer the short-term substitution rate, equilibrium base frequencies, and transition/transversion ratio).

MCC_*_standard.tree: Contains the inferred maximum clade credibility tree for * = HCV and sarbecovirus using the standard HKY+G substitution model.

MCC_*_&_%_PoWtransformed.tree: Contains the inferred maximum clade credibility tree for * = FV, HCV, and sarbecovirus using & = JC69 or HKY85 substitution models. This includes % = fixedRate or variedRate whereby the short-term rate and fastest-evolving rate groups are either fixed or varied.

*_&_%.xml: Contains the XML file for the * = FV, HCV, and sarbecovirus analyses of inferring & = distance or short-term substitution rates using % = JC69 or HKY85 substitution models.

HCV_alignments.FST: Contains the HCV alignments.