Releases: beast-dev/beast-mcmc
Release list
BEAST X v10.6.0-beta5
BEAST X v10.6.0 (in development)
New features
BEAUti
- Added option to write doubling time in days to the log file when using a coalescent model with an exponential growth parameter.
- Added an option to write the epidemiological reproduction number (R0) to the log file when using a coalescent model with an exponential growth parameter. This requires an estimate of the mean and standard deviation of the generation time distribution to be specified in BEAUti.
TreeAnnotator
- Can specify multiple HPD intervals e.g., using `--hpd 0.95,0.90,0.5'
- Can generate a KDE curve of the distribution of height values for visualisation in PearTree
- Clade MRCA heights can be calculated to avoid negative branch lengths (CA method of Heled and Bouckaert, (2013))
Bug fixes
BEAST
- Shows console window when running in Windows GUI version.
TreeAnnotator
-
Fixed TreeAnnotator not summarising 2-dimensional locations correctly —
continuous phylogeographic location traits (e.g.location1/location2)
were being renamed tolocation.rate1/location.rate2in the annotated
tree output.
(#1242) -
Fixed performance regression in TreeAnnotator "Collecting node information"
stage — processing of large tree sets became increasingly slow and eventually
stalled, a regression introduced after Beta5.
(#1233) -
Fixed bug in TreeAnnotator for continuous phylogeography with fixed trees —
coordinate annotations were being replaced by branch lengths and then discarded
when the input tree topology was fixed rather than sampled.
(#1255)
BEAUti
-
Fixed BEAUti reverting clock-rate prior to CTMC reference prior — custom
rate priors (e.g. a lognormal prior on the substitution rate) specified in
BEAUti were being silently replaced by the CTMC reference prior when the XML
was written.
(#1238) -
Fixed an issue where if the name stem was too long, the names of the log files and tree files could be truncated in the XML.
Other changes
- Updated HIPSTR citation to the final published paper.
(#1243)
Full Changelog: v10.5.0...v1.6.0-beta5
BEAST X v10.5.0
Open-source and cross-platform BEAST software combines molecular phylogenetic reconstruction with complex trait evolution, divergence-time dating and coalescent demographics in an efficient statistical inference engine.
BEAST X (v10.5.0) significantly advances the flexibility and scalability of evolutionary models supported. Novel clock and substitution models leverage: a large variety of evolutionary processes; discrete, continuous and mixed traits with missingness and measurement errors; and fast, gradient-informed integration techniques that rapidly traverse high-dimensional parameter spaces.
See http://beast.community/ for more details.
BEAST.X.v10.5.0.dmg – Mac OS X version
BEAST.X.v10.5.0.zip – Windows version
BEAST_X_v10.5.0.tgz – Linux/UNIX version
SARS-CoV-2-origins
BEAST software release for Pekar et al. (2022).
BEAST v1.10.5 pre-release of ThorneyTreeLikelihood v0.1.2
This release includes a few patches that have been made in the main branch since the last release, and makes the thorneytreelikelihood xml api more intuitive. Branch length likelihoods now take a branch rate model only.
Preview of PersistenceSummarizer
v1.10.5pre_persistence_summarizer_v0.1 bug fix for GSS when using GTR
BEAST v1.10.4
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 v1.10.3
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 v1.10.2
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 v1.10.1
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
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