ID	Type	Status	Priority	Milestone	Owner		Summary + Labels	...
	4	Enhancement	Accepted	Medium	----	rambaut		Feature request: Exponential Bayesian Skyline
	19	Enhancement	Accepted	Medium	----	rambaut		Setting lognormal priors in real-space
	20	Enhancement	Accepted	Medium	----	rambaut		Error reporting when parsing XML
	29	Defect	Accepted	Medium	----	alexei.drummond		Bug in AlignmentParser prevents the use of general data types
	40	Defect	Accepted	Medium	----	rambaut		TreeAnnotator produces misleading medians and HPDs when calculated from only 1 tree.   v1.4.6
	43	Defect	Accepted	Medium	----	jheled		treeTraceAnalysis fails due to comment in newick importer
	45	Defect	Accepted	Medium	----	jheled		Tracer BSR panel print command semi hangs (Linux)   tracer
	46	Defect	Accepted	Medium	----	jheled		BSP solid interval broken   tracer
	47	Other	Accepted	Medium	----	jheled		exp-const-exp model has deterioreted   tracer
	48	Defect	Accepted	Medium	----	jheled		TreeLogAnalyzer fails when run on log not analyzed by randomlocalclock model
	50	Defect	Accepted	Medium	----	jheled		Setting manual X axis in tracer takes forever to draw   Tracer v1.4.1
	51	Enhancement	Accepted	High	----	jheled		log-normal prior in beauti not that usefull presentation   v1.5beta beauti
	52	Defect	Accepted	Medium	----	rambaut		Commas put into years displayed in BEAUti   v1.4.7 beauti
	54	Defect	New	Medium	----	alexei.drummond		Loading templates in BEAUti sometime spontaneously changes mutation rate to be fixed to 1.0
	59	Defect	Assigned	Medium	----	alexei.drummond		examples/testCoalescent.xml
	62	Enhancement	New	Low	----	----		Feature Request: Restarting   beast
	64	Task	Accepted	Medium	----	victor.obolonkin		Fix all occurences of $Id$ to work with svn   Maintainability
	66	Defect	New	Medium	----	rambaut		BEAUti can't read NEXUS files produced by MacVector   v1.4.8
	71	Enhancement	Accepted	Medium	----	rambaut		Reflected exponentials (or lognormals) as priors?   v1.5beta2
	73	Enhancement	Accepted	Medium	----	jheled		Tracer usability improvment
	78	Defect	Accepted	Medium	----	jheled		Tracer development version - default directory not set for file selection
	83	Defect	Accepted	Medium	----	msuchard		Should SubStatistic starting counting from 1?
	85	Enhancement	Accepted	Medium	----	dong.w.xie		Add search filter above Included and Excluded taxa in Taxon Sets panel of BEAUti   v1.5beta3 beauti
	86	Defect	Accepted	Medium	----	rambaut		Error messages in BEAST are not consistent   v1.5beta3
	87	Enhancement	Accepted	High	----	rambaut		Improve error handling in BEAST   v1.5beta3
	88	Defect	Accepted	Medium	----	rambaut		LogCombiner should not allow thinning that is not compatible with the original sampling rate   v1.5beta3 logcombiner
	89	Defect	New	Medium	----	----		Beauti problem reading nexus files with quoted taxon names containing embedded square brackets   v1.5beta3 beauti
	90	Enhancement	Accepted	Medium	----	jheled		tracerbounding box color
	93	Enhancement	Accepted	Medium	----	dong.w.xie		BEAUTi defect regarding Logistic + Growth Rate prior, Autocorrelated Relaxed Clock, and Random Clock Model
	102	Enhancement	Accepted	Medium	----	rambaut		Comments and suggestions for "Trees Tab"   BEAUtiv1.5
	111	Task	Accepted	Medium	----	dong.w.xie		Video tutorial for BEAUTi and BEAST v1.5   BEASTv1.5
	112	Defect	Accepted	Medium	----	jheled		Beauti fails to read a nexus file
	113	Enhancement	Accepted	Medium	----	jheled		Beauti: allow to select multiple partition models: subst, clock, tree   BEAUTi1.5.1
	129	Defect	Accepted	Medium	----	dong.w.xie		BEAUTi: maximumTipHeight should be referred to each tree   BEAUTiv1.5
	130	Enhancement	Accepted	Medium	----	dong.w.xie		BEAUTi: prior setting should be assigned in its corresponding partition model.   BEAUTiv1.5
	132	Enhancement	Accepted	Low	----	dong.w.xie		BEAUTi: add JC in subsititution model
	137	Defect	Accepted	Medium	----	dong.w.xie		BEAUTi: ClockModelsPanel. JTable. setValueAt(...) fires twice   BEAUTiv1.5
	138	Defect	Accepted	Medium	----	jheled		likelihood.makeDirty is not suffcient
	141	Other	Accepted	Medium	----	jheled		AbstractNucleotideModel
	142	Defect	Accepted	Medium	----	dong.w.xie		Need xml validation for siteModel paser   BEASTv1.5
	143	Enhancement	Accepted	Medium	----	dong.w.xie		BEAUTi: tidy up the order in the log for better comparesion in Tracer   BEAUTiv1.5.1
	149	Enhancement	Accepted	High	----	dong.w.xie		Tracer: add another panel to plot auto-correlation   Tracer
	150	Enhancement	Accepted	Medium	----	dong.w.xie		BEAUTi: save current settings and use them for future analyses   BEAUTiv1.5.1
	152	Enhancement	Accepted	Medium	----	jheled		reporting from inside xml
	153	Enhancement	Accepted	Medium	----	jheled		Would be nice to have generic support for int,long,bool native internal BEAST parameter
	159	Task	Accepted	High	----	dong.w.xie		GTR parameter estimation test
	162	Enhancement	Accepted	Medium	----	dong.w.xie		Fix unstable JUnit test   JUnittest
	167	Enhancement	Accepted	Medium	----	beth.shapiro		Feature request: command-line BSP output from Tracer   Tracerv1.4.1
	170	Defect	Accepted	Medium	----	dong.w.xie		coalescentLikelihood -INF when using UPGMA starting tree   BEASTv1.5.1
	171	Enhancement	Accepted	Medium	----	dong.w.xie		Version update reminder in BEAUTi   BEAUTi1.5.1
	175	Enhancement	Accepted	Medium	----	dong.w.xie		Remove all rate node parameters from tree model   BEAST1.5.1
	177	Enhancement	Accepted	Medium	----	dong.w.xie		BEAUTi: a new Summary tab panel   BEAUTi1.5.1
	186	Defect	Accepted	Medium	----	rambaut		Guess Trait dialog has ambiguous text   BEAUtiv1.5.1
	187	Review	Accepted	Medium	----	rambaut		Unify reading and writing of trees for utility programs
	189	Defect	Accepted	Medium	----	jheled		Gamma quantile fails on values close to 0 or 1
	198	Defect	Accepted	Medium	----	dong.w.xie		Improper JUnit test code causes incorrect failure in Hudson   JUnit_Test
	206	Enhancement	Accepted	Medium	----	jheled		BEAUTi should support setting priors on species tree times   BEAUti v1.5.2
	210	Enhancement	Accepted	Medium	----	rambaut		Add ability to create columns in Tracer that are expressions of other columns   Tracer v1.4.1
	213	Defect	New	Medium	----	dong.w.xie		Missing lib files for AminoAcidLikelihoodCore, GeneralLikelihoodCore, CovarionLikelihoodCore, NativeLikelihoodCore   BEAST1.5.2
	224	Task	Accepted	Medium	----	dong.w.xie		Need to refactory dr.evomodel.arg.ARGModel, which has 4471 lines   BEAST1.5.2
	228	Defect	Accepted	Medium	----	jheled		LogCombiner mishandles trees with attributes   LogCombiner v1.5.2
	230	Defect	Accepted	Medium	----	dong.w.xie		Add beast.css for BEASTParserDoc   v1.5.2 BEASTDoc
	235	Defect	Accepted	Medium	----	rambaut		Unlinked DiscretizedBranchRates for multiple loci have the wrong number of dimensions   BEAUti v1.5.2
	243	Task	----	Medium	----	dong.w.xie		create a beast-core-trace.jar library to peel Tracer out of the BEAST   Tracer
	245	Other	New	Medium	----	----		*beast log files returns infinity for posterior and likelihood and a constant prior at aprox 22 million generations   BEAST v1.5.2
	246	Enhancement	Accepted	Medium	----	dong.w.xie		BEAUTi: weak HKY-like Dirichlet prior for GTR relative rates   BEAUTi v1.5.2
	249	Defect	New	Medium	----	----		GMRF Skyride - "skyride.popSize" and "skyride.precision" stuck on starting values, "gmrfBlockUpdateOperator" changes are never accepted   BEAST BEAUti v1.5.2
	263	Defect	Accepted	Medium	----	dong.w.xie		BEAST ARG bug   BEAST 1.5.2
	266	Defect	Accepted	Medium	----	dong.w.xie		BEAST: tree prior expansion + growth not working   BEAST 1.5.2
	269	Defect	Accepted	Medium	----	dong.w.xie		duplicate id in BEAST Parser Library html   v1.5.3 BEASTDoc
	273	Enhancement	New	High	----	dong.w.xie		Problems using Beast with blcr checkpointing   BEAST