danieljue beast-mcmc issues

danieljue / beast-mcmc

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

GNU Lesser General Public License v2.1

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Error when compiling from trunk using ant build 25-11-2013 (problem in CategoryOutbreak.java)

#713 GoogleCodeExporter closed 9 years ago
1
Conflict between antigenicLikelihood and cacheBranches=false

#712 GoogleCodeExporter closed 9 years ago
1
Sum constraints for Dirichlet distribution

#711 GoogleCodeExporter opened 9 years ago
2
Concurrency issues when two threads access the same tree likelihood

#710 GoogleCodeExporter opened 9 years ago
0
MCMC tab in Beautie v1.8.0 problem with multiple unlinked loci

#709 GoogleCodeExporter closed 9 years ago
2
Unable to use -beagle_AVX

#708 GoogleCodeExporter closed 9 years ago
2
Add integrable versions of Skyride and SkyGrid to facilitate path sampling

#707 GoogleCodeExporter opened 9 years ago
1
model selection and improper priors

#706 GoogleCodeExporter closed 9 years ago
4
Allow for recalculation of a subset of patterns

#705 GoogleCodeExporter opened 9 years ago
2
Guess dates function is affected by timezone of user

#704 GoogleCodeExporter closed 9 years ago
1
Error combining Markov jumps with codon partitioned substitution model

#703 GoogleCodeExporter closed 9 years ago
2
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

#702 GoogleCodeExporter closed 9 years ago
2
diffusionRateStatistic set-up in BEAuti

#701 GoogleCodeExporter closed 9 years ago
2
A lognormal-RRW in BEAuti in addition to the cauchy/gamma RRWs

#700 GoogleCodeExporter closed 9 years ago
2
BEAUti becomes unresponsive with 100s of partitions

#699 GoogleCodeExporter closed 9 years ago
1
Add a button to easy set precisions on multiple selected taxa.

#698 GoogleCodeExporter closed 9 years ago
1
Store/restore trouble with new BeagleTreeLikelihood

#697 GoogleCodeExporter closed 9 years ago
1
If I choose unlinked option for trees in partition alignment the algorithm will make one tree for each gene?

#696 GoogleCodeExporter closed 9 years ago
2
Implementing the Mk substitution model with BEAST and BEAGLE

#695 GoogleCodeExporter closed 9 years ago
1
BEAUti refresh error

#694 GoogleCodeExporter closed 9 years ago
4
Close all log files at the end of MCMC chain

#693 GoogleCodeExporter closed 9 years ago
2
PathSampling throws up an operator analysis after every iteration

#692 GoogleCodeExporter closed 9 years ago
1
Nexus importer doesn't allow spaces in nucleotide ranges

#691 GoogleCodeExporter closed 9 years ago
1
Tracer to support skygrid reconstructions

#690 GoogleCodeExporter closed 9 years ago
2
ConcurrentModificationException in SimpleOperatorSchedule.java

#689 GoogleCodeExporter closed 9 years ago
1
TreeAnnotator report selected tree

#688 GoogleCodeExporter closed 9 years ago
1
<rateCT> Missing from BEAUti GTR XML

#687 GoogleCodeExporter closed 9 years ago
2
Logistic growth shape vs t50

#686 GoogleCodeExporter opened 9 years ago
2
Creating multiple user starting trees for different partitions

#685 GoogleCodeExporter closed 9 years ago
1
Aspects of BEAUti model selection persists between windows

#684 GoogleCodeExporter closed 9 years ago
2
RandomWalkOperator is reflecting negative value to positive

#683 GoogleCodeExporter closed 9 years ago
5
Saving/loading files in BEAUti doesn't completely restore the model

#682 GoogleCodeExporter closed 9 years ago
2
BEASTMC3 app works. beastmc3 fails quietly.

#681 GoogleCodeExporter closed 9 years ago
6
Count state changes option in BEAUti doesn't generate a markovJumpsTreeLikelihood

#680 GoogleCodeExporter closed 9 years ago
2
TreeModels allows a leafHeight parameter to be replaced multiple times

#679 GoogleCodeExporter closed 9 years ago
1
BEAUti: add a "organelle (plants)" ploidy type with *BEAST

#678 GoogleCodeExporter opened 9 years ago
1
Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci

#677 GoogleCodeExporter closed 9 years ago
7
Attempting to open a file that isn't a BEAUti file will now display a message warning about loading a BEAST XML file.

#676 GoogleCodeExporter closed 9 years ago
0
The BirthDeath(Calibrated) model was not generating the calibration distribution model.

#675 GoogleCodeExporter closed 9 years ago
1
reciprocalStatistic requires an ID

#674 GoogleCodeExporter closed 9 years ago
2
BEAST Window closes before error message can be read

#673 GoogleCodeExporter closed 9 years ago
1
BEAUti duplicates rates in phylograms

#672 GoogleCodeExporter closed 9 years ago
2
Exporting taxon names in Nexus format - names with apostrophes are enclosed in single quotes

#671 GoogleCodeExporter closed 9 years ago
1
Discrete trait codes that are entirely numerical cause issues

#670 GoogleCodeExporter closed 9 years ago
1
AncestralTrait element should be able to log traits for tips.

#669 GoogleCodeExporter closed 9 years ago
1
Relaxed clock default should be continuous?

#668 GoogleCodeExporter opened 9 years ago
3
Dollo ambiguity code is incorrect when using BEAUti's no data option.

#667 GoogleCodeExporter closed 9 years ago
1
BEAUti should read charsets from sets blocks in NEXUS files

#666 GoogleCodeExporter closed 9 years ago
1
The coalescent based simulator doesn't respect hard bounds placed on MRCAs of taxon sets

#665 GoogleCodeExporter closed 9 years ago
1
Some priors are not being evaluated

#664 GoogleCodeExporter closed 9 years ago
1

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