beast-mcmc

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