marlichimi beast-mcmc issues

marlichimi / beast-mcmc

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Beauty gives empty String

#437 GoogleCodeExporter opened 8 years ago
0
BEAUti 1.6.1 sequenceErrorModel xml not work in BEAST

#436 GoogleCodeExporter closed 8 years ago
4
UniformIntegerOperator did not include upper in the value

#435 GoogleCodeExporter closed 8 years ago
1
BEAUti: Initial value missing from prior dialog

#434 GoogleCodeExporter closed 8 years ago
2
Typo in BEAUTi and example files

#433 GoogleCodeExporter closed 8 years ago
1
More detail for error message: *BEAST special part generation has failed.

#432 GoogleCodeExporter closed 8 years ago
1
BEAUTI 1.6.1 (Windows) and nothing happens

#431 GoogleCodeExporter closed 8 years ago
2
Implement Pearson Correlation Statistic

#430 GoogleCodeExporter closed 8 years ago
2
Specifying more than 2 -temperatures on the command line fails in parsing arguments

#429 GoogleCodeExporter closed 8 years ago
1
mc^3 does not respect preBurnin attribute in mcmc element

#428 GoogleCodeExporter closed 8 years ago
1
BEAUti generates a mergePatterns even when it is enclosing a single patterns element

#427 GoogleCodeExporter closed 8 years ago
1
BEAUti does not preserve model settings when re-linking

#426 GoogleCodeExporter closed 8 years ago
3
BEAUti can't re-link subst models anymore

#425 GoogleCodeExporter closed 8 years ago
4
TraitGuesser not extracting match within brackets (braces).

#424 GoogleCodeExporter closed 8 years ago
1
delta exchange operator discription is wrong

#423 GoogleCodeExporter closed 8 years ago
1
BEAUti: add validation to check whether modified prior initial value is between the boundary

#422 GoogleCodeExporter closed 8 years ago
1
Silent and inconsistent behaviour selecting unlinked Tree Prior

#421 GoogleCodeExporter closed 8 years ago
1
Add error message : Partitions cannot have the same name

#420 GoogleCodeExporter closed 8 years ago
1
BEAUti RealNumberField should not throw Exception all the time

#419 GoogleCodeExporter closed 8 years ago
1
Set maximun fraction digits for numbers displayed in BEAUti prior panel

#418 GoogleCodeExporter closed 8 years ago
1
BEAUti growthRate related XML causes -INF likelihood

#417 GoogleCodeExporter closed 8 years ago
1
Laplace prior parser should use scale same as BEAUti

#416 GoogleCodeExporter closed 8 years ago
2
Add "independent" column in BEAUti clock model panel table

#415 GoogleCodeExporter closed 8 years ago
3
BEAUti: incorrect xml for multi-alignment when given complex combination of clock model and tree model

#414 GoogleCodeExporter closed 8 years ago
2
BEAUti: duplicate class PartitionModelOptions causes model link conflict

#413 GoogleCodeExporter closed 8 years ago
1
BEAUti generates randomWalkOperator instead of randomWalkIntegerOperator for branchRates.categories

#412 GoogleCodeExporter closed 8 years ago
2
Incorrect validation and error message for random local clock in BEAUti

#411 GoogleCodeExporter closed 8 years ago
1
"Improper priors" on posterior statistics

#410 GoogleCodeExporter closed 8 years ago
2
BEAUti should explicitly generate uniform priors

#409 GoogleCodeExporter closed 8 years ago
3
TreeAnnotator crashes with Null Pointer Exception on malformed metacomment

#408 GoogleCodeExporter closed 8 years ago
3
*BEAST needs to log species tree in { }, otherwise TreeAnnotator keeps coming up with null exception on species tree

#407 GoogleCodeExporter closed 8 years ago
3
BEAST 1.6.0 GUI does not work with BEAGLE on Mac OSX 10.5

#406 GoogleCodeExporter closed 8 years ago
2
RandomWalkOperator with reflecting boundary can grind to a halt

#405 GoogleCodeExporter closed 8 years ago
2
Make "Median heights" as the default of nodeHeightsCombo

#404 GoogleCodeExporter closed 8 years ago
1
Starting tree generated with constraints by BEAUti is not correct XML for BEAST

#403 GoogleCodeExporter closed 8 years ago
3
BEAUti generates 0 size for subTreeSlide

#402 GoogleCodeExporter closed 8 years ago
1
BEUAti with 60 loci - pretty useless

#401 GoogleCodeExporter closed 8 years ago
3
Same as Issue 204 happened again in v1.6.x

#400 GoogleCodeExporter closed 8 years ago
6
Binary for TreeStat packaged with BEAST v1.6 has wrong version number and icon

#399 GoogleCodeExporter closed 8 years ago
1
BEAUti text message overlaps with button

#398 GoogleCodeExporter closed 8 years ago
3
*BEAST in BEAUti is broken

#397 GoogleCodeExporter closed 8 years ago
5
make alias "forParent" of "includeStem" in TMRCAPasrer

#396 GoogleCodeExporter closed 8 years ago
2
BEAUti: *BEAST check box should be unchecked after all data partition is deleted

#395 GoogleCodeExporter closed 8 years ago
1
Beuati fails to guess species names

#394 GoogleCodeExporter closed 8 years ago
2
Fix the message of the Bayes factor report in Tracer

#393 GoogleCodeExporter closed 8 years ago
1
BEAUti: wrong validation to apply Normal prior to tmrca

#392 GoogleCodeExporter closed 8 years ago
1
BEAUti: add forParent for taxon set

#391 GoogleCodeExporter closed 8 years ago
4
Tracer is broken

#390 GoogleCodeExporter closed 8 years ago
3
add TreeStat into BEAST release

#389 GoogleCodeExporter closed 8 years ago
2
BEAUti: "species" should NOT be used as a trait name

#388 GoogleCodeExporter closed 8 years ago
1