BEAST XML used in the reconstruction of the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008-2018

Below is the description of each file and folder:

• fullAeBspTmrca.xml
  • Phylodynamic analysis to estimate CRF01_AE tMRCA and N_e with BSP on full dataset of large CRF01_AE cluster
• fullAeBdsky.xml
  • Phylodynamic analysis to estimate CRF01_AE R_e with BDSKY on full dataset of large CRF01_AE cluster
• fullAeGeo.xml
  • Phylogeographic analysis to estimate CRF01_AE spatiotemporal spread with discrete trait substitution model on full dataset of large CRF01_AE cluster with both collection date and location metadata
• fullBBspTmrca.xml
  • Phylodynamic analysis to estimate subtype B tMRCA and N_e with BSP on full dataset of large subtype B cluster
• fullBBdsky.xml
  • Phylodynamic analysis to estimate subtype B R_e with BDSKY on full dataset of large subtype B cluster
• AeSubsamples
  • Phylodynamic analysis to estimate CRF01_AE R_e with BDSKY on two distinct uniform subsamples of the large CRF01_AE cluster
• GeoSensitivityAnalysis
  • Phylogeographic analysis on ten different subsamples each with equal number of CRF01_AE sequences per deme
• PsSs
  • Best-fit molecular clock model comparison using path sampling / stepping stone for CRF01_AE and subtype B datasets