This is a repository of analyses for the PANGEA-HIV Phylodynamics Methods Comparison exercise. Datasets and instructions can be found here. The intention of this repository is to generate trees, evolutionary rates, etc., so that more interesting things can be addressed in the (mere!) month for the first set of analyses to be completed.
- sequences: raw and processed sequence files
- raxmltrees: ML trees generated by RAxML
- lsd: clock-like trees generated by LSD, based on the RAxML trees
- mrbayestrees: input files for MrBayes and corresponding outputs
- phymltrees: input files for PhyML (assuming GTR+freerates(20))
- mixedmodel: BEAST XML files for Bethany's mixed epidemic model
- phytime: input files for phytime, using RAxML topologies rooted with rtt from ape
- skyride: skyrides based on LSD trees
- traits: M2 model fitting of M/F
- treeshape: Sackin's index and cherries for LSD trees
- treeshape_raxml: Sackin's index and cherries for RAxML trees