Allow the use of a native general likelihood core.  Change handling of TipPartialsModel change events so only affected nodes with TipPartialsModels get marked dirty -- saves lots of recompute. --------------- Adding a new model of hidden linkage among reads in a metagenomic dataset.  The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen.  This is one part of commit phase 2.  
Allow the use of a native general likelihood core.  Change handling of TipPartialsModel change events so only affected nodes with TipPartialsModels get marked dirty -- saves lots of recompute.
---------------
Adding a new model of hidden linkage among reads in a metagenomic dataset.  The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen.  This is one part of commit phase 2.  

git-svn-id: 67bc77c75b8364e4e9cdff0eb6560f5818674cd8@3594 ca793f91-a31e-0410-b540-2769d408b6a1

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