Stein et al 2015 - BEAST xml file for taxon-complete analyses

This xml file includes the alignments, specifications and additional taxonomic constraints used in the taxon-complete analyses. Additionally, this file includes the code that helped to resolve the convergence problems (low ESS values) stemming from a sparse molecular data matrix. The approach was developed by Dr. Joseph W. Brown and involves the following: 1. Create a new compoundParameter to update mean clock rates as a set see lines: 19329 - 19339 2. Comment out the upDownOperators for each mean clock rate see lines: 20378 - 20483 3. Create a new upDownOperator for the new compound parameter see lines: 20495 - 20504 Searching for “compoundParameterSetUp” (omitting the “”) within the .xml file will locate each of the edits associated with setting up the new compoundParameter for mean clock rates.