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@rambaut rambaut released this Aug 7, 2019 · 828 commits to master since this release

v1.10.5pre1

clean screen output
Assets 5

@rambaut rambaut released this Aug 6, 2019 · 828 commits to master since this release

v1.5.3-tempest

clean screen output
Assets 5

@rambaut rambaut released this Nov 14, 2018 · 2046 commits to master since this release

BEAST v1.10.4 fixes a bug when trying specify a burnin on the command line version of LogCombiner. It also introduces two new command line options specific to BEAGLE v3.1 (-beagle_threading_off and -beagle_thread_count).


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 documentation can be found here

Assets 5

@rambaut rambaut released this Oct 27, 2018 · 2086 commits to master since this release

BEAST v1.10.3 fixes an important bug where performance was degraded when using BEAGLE 3 on CPUs (compared with using BEAGLE 2 or using GPUs).


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 documentation can be found here

Assets 5

@rambaut rambaut released this Oct 6, 2018 · 2099 commits to master since this release

BEAST v1.10.2 is a minor bug fix release.


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 documentation can be found here

Assets 5

@rambaut rambaut released this Aug 9, 2018 · 2168 commits to master since this release

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 documentation can be found here

Assets 5

@rambaut rambaut released this Jun 11, 2018 · 2211 commits to master since this release

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 documentation can be found here

Assets 5

@rambaut rambaut released this Jun 17, 2016 · 3712 commits to master since this release

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.
Assets 5

@rambaut rambaut released this Feb 13, 2016 · 3910 commits to master since this release

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.
Assets 5
Sep 22, 2015
remove unncessary parameter in MEEM
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