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Add -X flag to all applications, so more memory can be allocated
Fix some OS X with Java 9+ anomalies
More robust OS X CUDA check
More robust launch scripts
Better error reporting
More robust package manager
TreeAnnotator handles taxa that are numbers now
Allow multiple -D arguments to BEAST, allows commas in user defined variables
Note that if you use this, there may be packages that are still not available. If you need to use an unavailable package, you can use BEAST v2.4.8 instead.
Ensure BeagleTreeLikelihood gives correct likelihood with RNA data.
Relabel buttons: "Guess" is now "Auto configure" in tip dates panel. "+" button on priors panel is now "+ Add Prior". More sensible default date value for taxa without date specified in tip dates panel. Make sure the appropriate tree is used in MRCAprior. Make sure tips with 'fixed' distributions imported from Nexus do not get estimated. Robustify NEXUS parser. Taxa could be duplicated in taxon list in NexusParser. Prevent accidentally cloning of up-down-all operator in StarBeast.
Default locale set to english so full stops are used in NEXUS output. Warn if Yule (or BD) conditions on root, but no root MRCAPrior is set. Robustify resume Suppress "Overwrite (Y/N)?" message when BEAST runs in console. Stop chain when encountering a +infinity posterior. Check that taxon set is specified when using RandomTree. Normalise stateNodes so XML characters ('"&<>) get escaped properly when writing state files.
Improved formatting of app list.
Now adds common ancestor height estimates as attributes.
Changed access levels of a few methods in nexus parser. Add Tree scale and ScaleOperator test. Add new Tree constructor from root node. Add support for input/output of non-binary trees. Add Input.set() method. BeautiAlignmentProvider getAlignments method added to facilitate scripting. TreeParser correctly parses tree edge length metadata, and improved error reporting.
BEAUti Starting trees can now be edited (default random, choice of cluster and newick trees) Allow alignments to be replaced, so old analyses can be used for new data Fix fasta file import bug that marked sequences as amino acid while it should be nucleotide Keep trees linked when splitting alignment on codon positions Automatically set estimate flag on shape when choosing rate categories Fix display of integer alignments BEAST Better documentation More robust XMLParser Prevent double counting of offset in ParametricDistribution.sample DensiTree version updated to v2.2.6