Assets 9

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

Aug 19, 2018
bump version, make sure OS X CUDA check succeeds #798
Mar 14, 2018
fix for DataTypeDeEncodeTest #599
Jul 17, 2017
update version history #716

@rbouckaert rbouckaert released this Jul 10, 2017 · 169 commits to master since this release

Assets 6

BEAUti

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.

BEAST

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.

Appstore

Improved formatting of app list.

TreeAnnotator

Now adds common ancestor height estimates as attributes.

API updates:

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.
Jul 10, 2017
Revert "create bigger range of up-down opeartors for clock models/trees 
#228" to guarantee backward compatibility for release #716

This reverts commit f05ce05.

@rbouckaert rbouckaert released this Apr 26, 2017 · 225 commits to master since this release

Assets 6
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
Apr 26, 2017
Merge pull request #688 from genomescale/patch-1
Normalise statenode strings