"ID","Type","Status","Priority","Milestone","Owner","Summary","AllLabels"
"763","Defect","Accepted","Medium","Release1.8.3","rambaut","BEAUti creates a subtree slide operator with size zero when data is invariable","BEAUti, Milestone-Release1.8.3, Priority-Medium, Type-Defect, v1.8.2"
"762","Defect","New","Medium","","","Spurious <coalescentEventsStatistic> block inserted in log when selecting skygrid","Priority-Medium, Type-Defect"
"761","Defect","New","Medium","Release1.6.1","rambaut","Tracer BSP plots missing 10^-1 labels","1.6, Milestone-Release1.6.1, Priority-Medium, Tracer, Type-Defect"
"760","Task","New","High","","rambaut","Export project to Github or another repo host","Priority-High, Type-Task"
"759","Defect","New","Low","","","4 taxa were in the xml file but error messages of ""Tree with fewer than 3 taxa"" by BEAST","Priority-Low, Type-Defect"
"756","Defect","Fixed","Medium","Release1.8.2","mdhall272","FEE with random local clock + codon position partitions + multiple threads","Milestone-Release1.8.2, Priority-Medium, Type-Defect, beast, v1.8.1"
"755","Defect","Invalid","Medium","","","BEAST disappears without error message on running xml BEAUti script","Priority-Medium, Type-Defect"
"754","Defect","Fixed","Critical","Release1.8.2","rambaut","BEAST v1.8.1 is not terminating leaving 'zombie' processes","Milestone-Release1.8.2, Priority-Critical, Type-Defect, beast, v1.8.1"
"753","Defect","Accepted","Low","","mdhall272","Tracer 1.6 has option for categorical data but still won't load non-numerical trace files","Priority-Low, Tracer-1.6, Type-Defect"
"752","Defect","Invalid","Medium","","","i am not able to run beast in Ubuntu server","Priority-Medium, Type-Defect"
"751","Defect","Accepted","Medium","Release1.8.2","mdhall272","Full evaluation error","Milestone-Release1.8.2, Priority-Medium, Type-Defect, beast, v1.8.1"
"750","Defect","Accepted","Medium","Release1.8.2","rambaut","-Infinity value always come out when i try to load xml","Milestone-Release1.8.2, Priority-Medium, Type-Defect, beast, v1.8.1"
"749","Defect","Fixed","Medium","Release1.8.2","rambaut","Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction","Milestone-Release1.8.2, Priority-Medium, Type-Defect, beauti, v1.8.1"
"748","Defect","WontFix","Medium","","","TreeAnnotator: Sum of clade credibility score for tree reported wrongly when burnin is == 0","Priority-Medium, Type-Defect"
"747","Defect","Fixed","Medium","Release1.8.2","msuchard","Duplicate references in robust counting with multiple partitions","Milestone-Release1.8.2, Priority-Medium, Type-Defect, beauti, v1.8.1"
"746","Patch","Fixed","","","","Allows you to have a custom $HOME/lib directory","Type-Patch"
"745","Defect","Fixed","Medium","Release1.8.2","rambaut","Removing an HPM from some parameters doesn't remove the model in the XML","1.8, Milestone-Release1.8.2, Priority-Medium, Type-Defect, beauti"
"744","Defect","Invalid","Medium","","","BEAUTI does not start","Priority-Medium, Type-Defect"
"743","Defect","Fixed","Medium","Release1.8.1","rambaut","Partitions in BEAUti should have the same number of taxa as the tree they are using.","Milestone-Release1.8.1, Priority-Medium, Type-Defect, beauti, v1.8.0"
"742","Defect","Invalid","Medium","","","invalid values during phylogeographic inference in continious space","Priority-Medium, Type-Defect"
"741","Defect","Fixed","Medium","Release1.8.1","philippe.lemey","Fix negative branch length issues when sampling taxa ages from precision, or set different (default) operator ","Milestone-Release1.8.1, Priority-Medium, Type-Defect"
"740","Enhancement","Fixed","Medium","Release1.8.1","philippe.lemey","Add jitter option to continuous diffusion options in the BEAUti sites panel","Milestone-Release1.8.1, Priority-Medium, Type-Enhancement"
"739","Defect","Accepted","Medium","Release1.8.1","mdhall272","Skygrid can reject all moves on popoulation sizes","Milestone-Release1.8.1, Priority-Medium, Type-Defect, beast, v1.8"
"738","Defect","New","Medium","Release1.9","","Beauti not retaining settings when saved file is reopened.","1.8, Milestone-Release1.9, Priority-Medium, Type-Defect, beauti"
"737","Defect","Accepted","Medium","Release1.6.1","mdhall272","Skyride reconstruction broken in Tracer 1.6","1.6, Milestone-Release1.6.1, Priority-Medium, Type-Defect, tracer"
"736","","Invalid","","","","doubts Divergence Dating",""
"735","Defect","Accepted","Medium","","mtolkoff","Row vs. Column Major in MatrixParameter Class","Priority-Medium, Type-Defect"
"734","Defect","Fixed","Medium","Release1.8.1","","BEAUti duplicates leafHeight parameters in multiple partition XMLs","1.8, Milestone-Release1.8.1, Priority-Medium, Type-Defect, beauti"
"733","Defect","Duplicate","Medium","","","Error random local clock","Priority-Medium, Type-Defect"
"732","Defect","Invalid","Medium","","","SericolaLatentStateBranchRateModel.java is precluding succeful build","Priority-Medium, Type-Defect"
"731","Enhancement","WontFix","Medium","","mdhall272","-seed option for MC3","Priority-Medium, Type-Enhancement"
"730","Patch","New","","","","Patch for /trunk/build_coalsim.xml","Type-Patch"
"729","Defect","Fixed","Low","Release1.8.1","mdhall272","Setting initial values for infinite uniform improper priors in BEAUTi","1.8, BEAUti, Milestone-Release1.8.1, Priority-Low, Type-Defect"
"728","Defect","Fixed","Medium","Release1.8.1","rambaut","Having taxon sets defined without heights when using a user starting tree causes parsing issues.","BEAUti, Milestone-Release1.8.1, Priority-Medium, Type-Defect, v1.8"
"727","Defect","Invalid","Medium","","mdhall272","NexusImporter and Markov Jumps CJH to tree","Priority-Medium, Type-Defect"
"726","Defect","Fixed","Medium","","","BinaryCovarionModelTest.java is impeding successful building","Priority-Medium, Type-Defect"
"725","Defect","Fixed","Medium","Release1.8.1","","BEAUti duplicates parameter id of Markov jumps for multiple traits.","1.8, Milestone-Release1.8.1, Priority-Medium, Type-Defect, beauti"
"724","Defect","Accepted","Medium","Release1.9","msuchard","Dollo model does not appear to parse under BEAGLE","Milestone-Release1.9, Priority-Medium, Type-Defect"
"723","Defect","Fixed","Medium","","msuchard","Conflict between -beagle_sse and -beagle_order/beagle_cuda","Priority-Medium, Type-Defect"
"722","Defect","Fixed","Medium","Release1.8.1","rambaut","Complex charsets in nexus files don't parse","BEAUti, Milestone-Release1.8.1, Priority-Medium, Type-Defect, v1.8"
"721","Enhancement","Accepted","Low","","alexander.alekseyenko","Create shortcuts for standard types of ascertainment","Priority-Low, Type-Enhancement"
"720","Defect","Fixed","Medium","","philippe.lemey","LeafTraitExtractorParser required for next beast release in order to be able to sample continuous leaf traits","Priority-Medium, Type-Defect"
"719","Defect","Fixed","Medium","","mdhall272","Markov Jumps parsing error","Priority-Medium, Type-Defect"
"718","Defect","WontFix","Medium","Release1.8.1","rambaut","Bug in BEAUti which prevents it from emitting the updown operator in some cases, which can slow convergence","BEAUti, Milestone-Release1.8.1, Priority-Medium, Type-Defect"
"717","Defect","Accepted","Medium","Release1.7","rambaut","Tracer not rescaling trace plot for multiple traces","1.6, Milestone-Release1.7, Priority-Medium, Tracer, Type-Defect"
"716","Defect","New","Medium","","","BEAST microsatellite input format","Priority-Medium, Type-Defect"
"715","Defect","Fixed","Medium","","philippe.lemey","TransformedTreeModelParser not part of BEAST1.8 (to run Pagel's lambda estimator)","Priority-Medium, Type-Defect"
"714","Defect","Fixed","Medium","Release1.8.1","","sets block not recognized in 1.8","Beauti, Milestone-Release1.8.1, Priority-Medium, Type-Defect, v1.8"
"713","Defect","Fixed","Medium","","","Error when compiling from trunk using ant build 25-11-2013 (problem in CategoryOutbreak.java)","Priority-Medium, Type-Defect"
"712","Defect","Fixed","Medium","","trevor@bedford.io","Conflict between antigenicLikelihood and cacheBranches=false","Priority-Medium, Type-Defect"
"711","Defect","Accepted","Medium","Release1.9","msuchard","Sum constraints for Dirichlet distribution","Milestone-Release1.9, Priority-Medium, Type-Defect"
"710","Defect","Accepted","Medium","","rambaut","Concurrency issues when two threads access the same tree likelihood","BEAST, Priority-Medium, Type-Defect, v1.8"
"709","Defect","Fixed","Medium","Release1.8.1","","MCMC tab in Beautie v1.8.0 problem with multiple unlinked loci","1.8, Milestone-Release1.8.1, Priority-Medium, Type-Defect, beauti"
"708","Defect","WontFix","Medium","","","Unable to use -beagle_AVX","Priority-Medium, Type-Defect"
"707","Enhancement","Accepted","Medium","Release1.9","msuchard","Add integrable versions of Skyride and SkyGrid to facilitate path sampling","Milestone-Release1.9, Priority-Medium, Type-Enhancement"
"706","Enhancement","Fixed","Medium","Release1.8","","model selection and improper priors","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Enhancement"
"705","Enhancement","Accepted","Medium","","alexander.alekseyenko","Allow for recalculation of a subset of patterns","Priority-Medium, Type-Enhancement"
"704","Defect","Fixed","Medium","Release1.8","rambaut","Guess dates function is affected by timezone of user","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"703","Defect","Fixed","Medium","Release1.8","baele.guy","Error combining Markov jumps with codon partitioned substitution model","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"702","Defect","Fixed","Medium","Release1.8","philippe.lemey","set the cmctScale prior as default for the trait.clock.rate in discrete trait analysis in BEAuti and include the estimation of root frequencies in the nonreversible model","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"701","Enhancement","Fixed","Medium","Release1.8","philippe.lemey","diffusionRateStatistic set-up in BEAuti","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Enhancement, v1.7.5"
"700","Enhancement","Fixed","Medium","Release1.8","philippe.lemey","A lognormal-RRW in BEAuti in addition to the cauchy/gamma RRWs","1.7.5, BEAUti, Milestone-Release1.8, Priority-Medium, Type-Enhancement"
"699","Defect","Fixed","Medium","Release1.8","rambaut","BEAUti becomes unresponsive with 100s of partitions","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"698","Defect","Fixed","Medium","Release1.8","rambaut","Add a button to easy set precisions on multiple selected taxa.","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"697","Defect","Fixed","Medium","Release1.8","msuchard","Store/restore trouble with new BeagleTreeLikelihood","Milestone-Release1.8, Priority-Medium, Type-Defect"
"696","Other","Invalid","Medium","","","If I choose unlinked option for trees in partition alignment the algorithm will make one tree for each gene?","Priority-Medium, Type-Other"
"695","Defect","Fixed","Medium","Release1.8","","Implementing the Mk substitution model with BEAST and BEAGLE","Milestone-Release1.8, Priority-Medium, Type-Defect"
"694","Defect","Duplicate","Medium","Release1.8","rambaut","BEAUti refresh error","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.4"
"693","Defect","Fixed","Medium","Release1.8","rambaut","Close all log files at the end of MCMC chain","1.7.4, Milestone-Release1.8, Priority-Medium, Type-Defect, beast"
"692","Defect","Fixed","Medium","Release1.8","rambaut","PathSampling throws up an operator analysis after every iteration","Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.4"
"691","Defect","Fixed","Medium","Release1.8","rambaut","Nexus importer doesn't allow spaces in nucleotide ranges","1.7.5, Milestone-Release1.8, Priority-Medium, Type-Defect"
"690","Enhancement","Fixed","Medium","Release1.8","msuchard","Tracer to support skygrid reconstructions","Milestone-Release1.8, Priority-Medium, Type-Enhancement"
"689","Defect","Fixed","Medium","","","ConcurrentModificationException in SimpleOperatorSchedule.java","Priority-Medium, Type-Defect"
"688","Patch","Fixed","","","","TreeAnnotator report selected tree","Type-Patch"
"687","Defect","Invalid","Medium","","","<rateCT> Missing from BEAUti GTR XML","Priority-Medium, Type-Defect"
"686","Defect","Accepted","Medium","Release1.7","trevor@bedford.io","Logistic growth shape vs t50","Milestone-Release1.7, Priority-Medium, Type-Defect, tracer"
"685","Defect","Fixed","Medium","Release1.8","rambaut","Creating multiple user starting trees for different partitions","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"684","Defect","Fixed","Medium","Release1.8","rambaut","Aspects of BEAUti model selection persists between windows","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"683","Defect","Fixed","Medium","","msuchard","RandomWalkOperator is reflecting negative value to positive","Priority-Medium, Type-Defect"
"682","Defect","Fixed","Medium","Release1.8","rambaut","Saving/loading files in BEAUti doesn't completely restore the model","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"681","Defect","Fixed","Medium","Release1.8","trevor@bedford.io","BEASTMC3 app works.  beastmc3 fails quietly.","Milestone-Release1.8, Priority-Medium, Type-Defect, beast, v1.7.5"
"680","Defect","Fixed","Medium","Release1.8","rambaut","Count state changes option in BEAUti doesn't generate a markovJumpsTreeLikelihood","BEAUti, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"679","Defect","Duplicate","Medium","Release1.8","rambaut","TreeModels allows a leafHeight parameter to be replaced multiple times","BEAST, Milestone-Release1.8, Priority-Medium, Type-Defect, v1.7.5"
"678","Enhancement","New","Medium","","","BEAUti: add a ""organelle (plants)"" ploidy type with *BEAST","Priority-Medium, Type-Enhancement"
"677","Defect","Fixed","Medium","Release1.7.6","dong.w.xie","Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci","BEAUti, Milestone-Release1.7.6, Priority-Medium, Type-Defect"
"676","Defect","Fixed","Medium","Release1.7.5","rambaut","Attempting to open a file that isn't a BEAUti file will now display a message warning about   loading a BEAST XML file. ","BEAUti, Milestone-Release1.7.5, Priority-Medium, Type-Defect, v1.7.4"
"675","Defect","Fixed","Medium","Release1.7.5","rambaut","The BirthDeath(Calibrated) model was not generating the calibration distribution model.","BEAUti, Milestone-Release1.7.5, Priority-Medium, Type-Defect, v1.7.4"
"674","Defect","Fixed","Low","","mdhall272","reciprocalStatistic requires an ID","Priority-Low, Type-Defect"
"673","Defect","Invalid","Medium","","rambaut","BEAST Window closes before error message can be read","BEAST, Priority-Medium, Type-Defect, v1.7.4"
"672","Defect","Fixed","Medium","Release1.7.5","","BEAUti duplicates rates in phylograms","BEAST, Milestone-Release1.7.5, Priority-Medium, Type-Defect, v1.7.4"
"671","Defect","Fixed","Medium","Release1.7.5","rambaut","Exporting taxon names in Nexus format - names with apostrophes are enclosed in single quotes","Milestone-Release1.7.5, Priority-Medium, Type-Defect, beast, v1.7.4"
"670","Defect","Invalid","Medium","","rambaut","Discrete trait codes that are entirely numerical cause issues","BEAST, Priority-Medium, Type-Defect"
"669","Enhancement","Invalid","Medium","Release1.7.5","rambaut","AncestralTrait element should be able to log traits for tips.","BEAST, Milestone-Release1.7.5, Priority-Medium, Type-Enhancement"
"668","Enhancement","Accepted","Medium","Release1.9","Sibon.Li","Relaxed clock default should be continuous? ","BEAUti, Milestone-Release1.9, Priority-Medium, Type-Enhancement"
"667","Defect","Fixed","Medium","Release1.7.5","msuchard","Dollo ambiguity code is incorrect when using BEAUti's no data option.","Milestone-Release1.7.5, Priority-Medium, Type-Defect"
"666","Defect","Fixed","Medium","Release1.7.5","rambaut","BEAUti should read charsets from sets blocks in NEXUS files","1.7.4, BEAUti, Milestone-Release1.7.5, Priority-Medium, Type-Defect"
"665","Defect","Fixed","Medium","Release1.7.5","rambaut","The coalescent based simulator doesn't respect hard bounds placed on MRCAs of taxon sets","1.7.4, BEAUti, Milestone-Release1.7.5, Priority-Medium, Type-Defect"
"664","Defect","Fixed","Medium","Release1.7.4","rambaut","Some priors are not being evaluated","BEAST, Milestone-Release1.7.4, Priority-Medium, Type-Defect, v1.7.3"
"663","Enhancement","Fixed","Medium","Release1.8","rambaut","Add new command line option to specify the precision to which the full evaluation checks are made.","BEAST, Milestone-Release1.8, Priority-Medium, Type-Enhancement, v1.7.3"
"662","Defect","Fixed","Medium","Release1.7.5","","problem with reconstructing synonymous/non-synonymous change counts","BEAST, Milestone-Release1.7.5, Priority-Medium, Type-Defect"
This file is truncated to 100 out of 754 total results.  See https://code.google.com/p/beast-mcmc/issues/csv?can=1&q=&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Summary%20AllLabels&sort=-id&start=100 for the next set of results.
