@rambaut rambaut released this Feb 13, 2016 · 1898 commits to master since this release

Assets 5

Version 1.8.3 released 13th February 2016

New Features:
    Generalized Stepping Stone sampling for Marginal Likelihood Estimation.
    Continuous quantile version of uncorrelated relaxed clock as option in
    BEAUti [from Li & Drummond 2012, MBE].
    Option in BEAUti to log complete histories in Markov Jump Counting.
    Jukes-Cantor added as an option for BEAUti nucleotide substition model.
    New tree transition kernel (SubTreeLeap operator) implementd in BEAST.
    Defaulting to randomizing rate categories for DiscretizedBranchRates.
    BEAUti 'guess dates' options are now persistent from run to run (and
    shared with Path-O-Gen/Tempest).
    Transmission tree model of Hall et al (2016) implemented.
    Fast, general multidimensional scaling (MDS) implemented.
    Clock panel in BEAUti simplified.
    Parameter linking available in Priors panel in BEAUti.
    Command line is logged into log file headers for reference.

Bug Fixes:
    Issue 779:  Ancestral sequence reconstruction broken with
                <mergePatterns> elements.
    Issue 772:  BEAUTi should include BranchRatesModels in prior density.
    Issue 768:  BEAUti creates a subtree slide operator with size zero when
                data is invariable.
    Issue 758:  Full evaluation error.
    Issue 304:  Label individual transition rate dimensions for CTM models
                in log files.