README.md

Discete Trait Analysis

To understand global spread of mpox, we employ phylogeographic models to estimate the rates of migration between our five studied regions.

import main_masked_prevalence_subsampling_alignment.fasta from alignments into BEAUTI (v. 1.10.4)
infer tip dates
non-default model parameters:
- SITES/site heterogeneity model: gamma with 4 sites
- TREES/tree prior: coalescent bayesian Skygrid with 1.5 years before latest tip and 75 change points to allow for the effective population size to change every two weeks
- PRIORS/clock.rate: uniform prior with lower 0, upper 1.0, initial 6E-5
- MCMC/length of chain: 50000000
- MCMC/log parameters every: 25000
export xml

All xmls used in this project can be found in xmls.

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

Maximum clade credibility trees can be analyzed here while imports, exports, and persistence times can be analyzed here