What is new in BEAST v2.1.2 and its packages

31 March 2014 by Remco Bouckaert

BEAUti has many bug fixes and enhancements for supporting multiple paritions better. In particular, you can now clone site models and clock models; just select a set of models from the list in the Site Model or Clock Model panel, and the rest of the panel is filled with a “Clone From” selector. This makes it much easier to set all site models to say HKY + 4 gamma categories with estimated frequencies.

The AddOnManager has gotten a facelift. Dependent packages can be automatically installed and uninstalled. You can specify other package repositories than the default one that BEAST uses.

BEAUti can now import FASTA files next to NEXUS files and alignments from BEAST1 and BEAST2 XML files.

SequenceSimulator and LogAnalyser are enhanced to support simulation studies (more on this soon in this blog).

Distributions can be marked stochastic, so when the MCMC inner loop does a sanity check to ensure the incrementally calculated posterior remains the same as a freshly calculated posterior, these distributions can be ignored.

BEAUti automatically updates weights of *BEAST related operators so that the total times spent on *BEAST operators is 20%. This is believed to enhance *BEAST mixing.

New in BEAST-packages

To access packages, you should install them using the install them first.

New in BEAST-labs

BEAST-labs — formerly known as BEASTii — now contains a Script class that allows you to use Javascript (as well as other script languages like python and ruby, provided the appropriate script engine is in the class path). With a Script object you can log complex information that would otherwise require writing a new Java class.

Path sampling/stepping stone analyses is moved to the model selection package.

New in model-selection package

The model-selection package supports path sampling/stepping stone analyses. There is a simple GUI for setting up a path sampling/stepping stone analysis.

The package supports pairwise path sampling/stepping stone analysis where you can estimate the difference of marginal likelihood between two models. This is in general more efficient than estimating marginal likelihoods for each of the two models appart.

New in SNAPP

SNAPP now contains a simple SNP caller — it looks at the first sequence in the alignment, and assumes that the characters there represent the zero value for the site. This means you can use a nucleotide sequence directly in a SNAPP analysis, instead of having to convert it to a binary sequence first.

Tip texts in BEAUti are improved.

New in BDSKY

Robustify against incorrect input, and remove intervalNumber-input.

New packages

Some new packages were added: