Beast Mcmc Versions Save

BEAST software release for Pekar et al. (2022).

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.

This release includes a small patch for a bug which caused root height estimations to be biased towards grid points when intervals were passed directly to the skygrid as is done when using BigFastTreeIntervals.

This release adds a few very minor changes to the previous thorneyLikelihood pre-release. The first two should make trouble-shooting analyses easier. The third is only mentioned for completeness.

1. Topological operators select polytomies to resolve more efficiently
2. Topological operators exit gracefully if given a fully resolved tree
3. The constrained treeModel is now a fully fledged tree model which removes the need for multiple tree models to exist for the duration of the run.

This pre-release includes recent work targeted at analyzing large SARS-CoV-2 datasets.

It also includes an updated pre-release of BEASTGen which is a useful command line utility for creating xml files based on the Apache FreeMarker template engine.

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

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

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