updating readme

README.md

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-# SARS-CoV-2_EUR_PHYLOGEOGRAPHY
+# SARS-CoV-2_EUR_PHYLOGEOGRAPHY
+repo associated with a manuscript on SARS-CoV-2 phylogeographic spread in western Europe.
+
+The XMLs can be run using the hmc-develop branch of the BEAST codebase available at https://github.com/beast-dev/beast-mcmc.
+- SC2eur_thGLM3cov.xml: requires the genome data from GISAID.org. Joint sequence and location inference using a discrete trait GLM with three time-homogeneous covariates
+- SC2eur_epoch3covHomoCoeff.xml: uses empirical.trees and includes three time-inhomogeneous covariates
+- SC2eur_epoch3covHierarchIncl.xml: uses empirical.trees and includes three time-inhomogeneous covariates along with time-inhomogeneous inclusion probabilities with a hierarchical graph prior
+- SC2eur_epochTHREs.xml: uses empirical.trees and includes three time-inhomogeneous covariates, time-homogeneous random effects, and epoch rate scalars that are a function of the overall mobility data.