mascot_glm

Phylodynamic Analysis

About the Analysis

To understand mpox transmission within and between regions studied, we employ an approximate structured coalescent approach called MASCOT-GLM which also uses generalized linear models to inform estimates of effective population size and migration rates. More information can found in Müller et al

Running the analysis

main analysis using GLM

1. import 500_unmasked_equal_temporal_mascot.fasta from alignments into BEAUTI
2. infer tip dates
3. non-default model parameters:
   • SITES/site heterogeneity model: gamma with 4 sites
   • TREES/tree prior: MASCOT-GLM
   • empirical predictors can be found in data which includes region_cases_weekly_prevalence.csv, month_predictor_1-9.csv, and regions_air_travel_matrix.csv
   • PRIORS/clock.rate: uniform prior with lower 0, upper 1.0, initial 6E-5
   • MCMC/length of chain: 50000000
   • MCMC/log parameters every: 25000
4. export xml

All xmls used in this project can be found in xmls and include manual xml edits to add in CoupledMCMC for faster convergence

All results for main and supplementary analyses can be found in results.

Maximum clade credibility trees and effective population sizes can be analyzed here while percentage of cases due to introductions and Rt over time can be analyzed here

XMLs and results for MASCOT-Skyline which is an approximation of the structured coalescent with a Skyline prior but without the influence of empirical predictors can be found in both xmls/ and results/ under the subfolder skyline/