The parametric plots in the Prior Dialog now show correctly. Improved speed of relaxed clock by more judicious updating of the likelihood when rates change on a few branches. Slight improvement in speed calculating the coalescent prior.
This will help comparisons of trees files using certain software that assume taxon orders are the same namely AWTY. Log normal prior element required meanInRealSpace attribute which prevented older XML file from running without modification.
This attribute is now optional. The Yule tree prior was wrongly implemented. BEAUti did not allow some types of compatable monophyly constraints. BEAST did not always simulate starting trees with enforced monophyly correctly.
BEAST ignored specified offsets for exponential priors on parameters. BEAUti ignored user specified offsets for gamma distribution priors on parameters. Taxon sets can now have monophyly enforced using BEAUti. Starting tree is now compatible with monophyly constraints and uniform priors on tMRCAs.
Relaxed clock statistics meanRate, etc. Fixed problem with rate estimation under the 2 partition codon specific rates models including SRD BEAUti did not accept the number of skyline groups properly. Fixed a problem using exponential distribution as priors. LogCombiner could mix up taxon labels when combining multiple tree files.
This problem would not affect the reconstruction of skyline plots. Faster likelihood calculations after rejecting a state. Whilst the improvement in speed will vary, the indications are that this is a significant overall speed improvement.
Rates for relaxed clock models can be written embedded in the tree for later analysis. BEAUti can be run non-interactively as a command-line using the template files. BEAUti did not use the specified fixed substitution rate. Fixed a problem with BEAUti not loading data when using a non-english operating system. Fixed a problem using gamma distribution as priors.
Problem with distributionLikelihood including all data twice resulting in the distributions being too tight. Improved error reporting. Logistic demographic model. Amino Acid models were not being set correctly resulting in the use of an equal-rates model.
Can now switch autoOptimize on or off for individual operators. This overrides the setting for the element. Default weights for certain operators have been changed in BEAUti to improve performance. An auto-optimize function that removes the need to perform manual tuning of operators. Improvement in speed of likelihood calculations for nucleotides. In future these will be distributed together with matching version numbers. Improved tree log analyser. Fixed the wrong coalescent likelihood function introduced in the last version.
Version History. Issue 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 Calculating pairwise distances was slow for big data sets - removed this but initial values no longer suggested based on data.
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