Bayesian Evolutionary Analysis Sampling Trees
BEAST v1.10.1 is a minor bug fix release.
Fixes issues with selecting the GTR model in BEAUti and running under Java 10 on Macs.
BEAST v1.10 is a major new version with many new features focusing on flexibility of model specification, integration of different data sources, and increasing the speed and efficiency of sampling.
The new version coincides with the publication of a paper describing many of the new features:
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ & Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evolution 4, vey016. DOI:10.1093/ve/vey016
BEAST v1.10 is a major new version with many new features focusing on flexibility of model specification, integration of different data sources, and increasing the speed and efficiency of sampling.
The new version coincides with the publication of a paper describing many of the new features:
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ & Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evolution 4, vey016. DOI:10.1093/ve/vey016
Version 1.8.4 released 17th June 2016
New Features:
New structured list of citations printed to screen before running.
Option ('-citation_file') to write citation list to file.
Option in BEAUti Priors panel to set parameters to 'Fixed Value'
Bug Fixes:
Issue 808: Set autoOptimize to false in the randomWalkOperator on
Pagel's lambda
Issue 806: SRD06 in BEAUTi selecting incorrect options.
Issue 799: Relative rate parameters for partitions were not being
created. All partitions within a clock model have a
relative rate if their substitution models are unlinked.
Issue 798: Calculating pairwise distances was slow for big data sets -
removed this (but initial values no longer suggested based
on data).
Issue 797: Removed 'meanRate' from Priors tab in BEAUti.
Issue 794: Running with empty command line causes error.
Issue 792: Check to see that the same likelihood isn't included multiple
times into the density.
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.
2015-03-05 - v1.8.2 Bugs fixed: Issue 747: Robust counting with multiple partitions generates unique reference IDs in BEAUti and unique total counts for Tracer. Issue 756: FEE with random local clock + codon position partitions + multiple threads. Issue 754: BEAST v1.8.1 is not terminating leaving 'zombie' processes Issue 749: Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction. Issue 747: Duplicate references in robust counting with multiple partitions. Issue 745: Removing an HPM from some parameters doesn't remove the model in the XML