JifengJiang beast-mcmc issues

JifengJiang / beast-mcmc

Automatically exported from code.google.com/p/beast-mcmc

GNU Lesser General Public License v2.1

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BEAUti creates a subtree slide operator with size zero when data is invariable

#763 GoogleCodeExporter opened 8 years ago
0
Spurious <coalescentEventsStatistic> block inserted in log when selecting skygrid

#762 GoogleCodeExporter opened 8 years ago
0
Tracer BSP plots missing 10^-1 labels

#761 GoogleCodeExporter opened 8 years ago
0
Export project to Github or another repo host

#760 GoogleCodeExporter opened 8 years ago
0
4 taxa were in the xml file but error messages of "Tree with fewer than 3 taxa" by BEAST

#759 GoogleCodeExporter opened 8 years ago
1
[deleted issue]

#758 GoogleCodeExporter closed 8 years ago
0
[deleted issue]

#757 GoogleCodeExporter closed 8 years ago
0
FEE with random local clock + codon position partitions + multiple threads

#756 GoogleCodeExporter closed 8 years ago
3
BEAST disappears without error message on running xml BEAUti script

#755 GoogleCodeExporter closed 8 years ago
2
BEAST v1.8.1 is not terminating leaving 'zombie' processes

#754 GoogleCodeExporter closed 8 years ago
1
Tracer 1.6 has option for categorical data but still won't load non-numerical trace files

#753 GoogleCodeExporter opened 8 years ago
0
i am not able to run beast in Ubuntu server

#752 GoogleCodeExporter closed 8 years ago
2
Full evaluation error

#751 GoogleCodeExporter opened 8 years ago
5
-Infinity value always come out when i try to load xml

#750 GoogleCodeExporter opened 8 years ago
8
Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction

#749 GoogleCodeExporter closed 8 years ago
2
TreeAnnotator: Sum of clade credibility score for tree reported wrongly when burnin is == 0

#748 GoogleCodeExporter closed 8 years ago
2
Duplicate references in robust counting with multiple partitions

#747 GoogleCodeExporter closed 8 years ago
2
Allows you to have a custom $HOME/lib directory

#746 GoogleCodeExporter closed 8 years ago
1
Removing an HPM from some parameters doesn't remove the model in the XML

#745 GoogleCodeExporter closed 8 years ago
2
BEAUTI does not start

#744 GoogleCodeExporter closed 8 years ago
1
Partitions in BEAUti should have the same number of taxa as the tree they are using.

#743 GoogleCodeExporter closed 8 years ago
1
invalid values during phylogeographic inference in continious space

#742 GoogleCodeExporter closed 8 years ago
2
Fix negative branch length issues when sampling taxa ages from precision, or set different (default) operator

#741 GoogleCodeExporter closed 8 years ago
1
Add jitter option to continuous diffusion options in the BEAUti sites panel

#740 GoogleCodeExporter closed 8 years ago
3
Skygrid can reject all moves on popoulation sizes

#739 GoogleCodeExporter opened 8 years ago
1
Beauti not retaining settings when saved file is reopened.

#738 GoogleCodeExporter opened 8 years ago
5
Skyride reconstruction broken in Tracer 1.6

#737 GoogleCodeExporter opened 8 years ago
1
doubts Divergence Dating

#736 GoogleCodeExporter closed 8 years ago
1
Row vs. Column Major in MatrixParameter Class

#735 GoogleCodeExporter opened 8 years ago
0
BEAUti duplicates leafHeight parameters in multiple partition XMLs

#734 GoogleCodeExporter closed 8 years ago
3
Error random local clock

#733 GoogleCodeExporter closed 8 years ago
2
SericolaLatentStateBranchRateModel.java is precluding succeful build

#732 GoogleCodeExporter closed 8 years ago
2
-seed option for MC3

#731 GoogleCodeExporter closed 8 years ago
1
Patch for /trunk/build_coalsim.xml

#730 GoogleCodeExporter opened 8 years ago
0
Setting initial values for infinite uniform improper priors in BEAUTi

#729 GoogleCodeExporter closed 8 years ago
2
Having taxon sets defined without heights when using a user starting tree causes parsing issues.

#728 GoogleCodeExporter closed 8 years ago
1
NexusImporter and Markov Jumps CJH to tree

#727 GoogleCodeExporter closed 8 years ago
2
BinaryCovarionModelTest.java is impeding successful building

#726 GoogleCodeExporter closed 8 years ago
2
BEAUti duplicates parameter id of Markov jumps for multiple traits.

#725 GoogleCodeExporter closed 8 years ago
2
Dollo model does not appear to parse under BEAGLE

#724 GoogleCodeExporter opened 8 years ago
1
Conflict between -beagle_sse and -beagle_order/beagle_cuda

#723 GoogleCodeExporter closed 8 years ago
2
Complex charsets in nexus files don't parse

#722 GoogleCodeExporter closed 8 years ago
2
Create shortcuts for standard types of ascertainment

#721 GoogleCodeExporter opened 8 years ago
0
LeafTraitExtractorParser required for next beast release in order to be able to sample continuous leaf traits

#720 GoogleCodeExporter closed 8 years ago
1
Markov Jumps parsing error

#719 GoogleCodeExporter closed 8 years ago
1
Bug in BEAUti which prevents it from emitting the updown operator in some cases, which can slow convergence

#718 GoogleCodeExporter closed 8 years ago
5
Tracer not rescaling trace plot for multiple traces

#717 GoogleCodeExporter opened 8 years ago
1
BEAST microsatellite input format

#716 GoogleCodeExporter opened 8 years ago
0
TransformedTreeModelParser not part of BEAST1.8 (to run Pagel's lambda estimator)

#715 GoogleCodeExporter closed 8 years ago
1
sets block not recognized in 1.8

#714 GoogleCodeExporter closed 8 years ago
2