Fixed an issue where once a 'substitutions' TreeLogger was created all subsequent TreeLoggers were also using the same BranchRates model to do substitution trees. This was an issue in the parser. The issue would not manifest itself if the substitutions tree log was the last in the XML (as generated by BEAUti).
Fixed an issue where once a 'substitutions' TreeLogger was created all subsequent TreeLoggers were also using the same BranchRates model to do substitution trees. This was an issue in the parser. The issue would not manifest itself if the substitutions tree log was the last in the XML (as generated by BEAUti).

git-svn-id: 67bc77c75b8364e4e9cdff0eb6560f5818674cd8@4500 ca793f91-a31e-0410-b540-2769d408b6a1

svn2github/beast-mcmc,armanbilge/BEAST_sandbox,svn2github/beast-mcmc,armanbilge/BEAST_sandbox,armanbilge/BEAST_sandbox,svn2github/beast-mcmc,svn2github/beast-mcmc,armanbilge/BEAST_sandbox,armanbilge/BEAST_sandbox,svn2github/beast-mcmc