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katylettuce
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beast-mcmc
Automatically exported from code.google.com/p/beast-mcmc
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Add new command line option to specify the precision to which the full evaluation checks are made.
#663
GoogleCodeExporter
closed
9 years ago
6
problem with reconstructing synonymous/non-synonymous change counts
#662
GoogleCodeExporter
closed
9 years ago
1
Fails to generate XML after particular sequence of options
#661
GoogleCodeExporter
closed
9 years ago
1
For trait specification errors, error messages should include name of taxon.
#660
GoogleCodeExporter
closed
9 years ago
1
BEAUti not setting dataType specific ambiguity codes in outputted alignments
#659
GoogleCodeExporter
closed
9 years ago
4
On line tutorials need refreshing
#658
GoogleCodeExporter
opened
9 years ago
0
review EBSP tutorial
#657
GoogleCodeExporter
closed
9 years ago
2
fix p=0 in Birth Death Serial Sampling Model
#656
GoogleCodeExporter
closed
9 years ago
1
Operator log sometimes attempts to write to locked folder causing exception
#655
GoogleCodeExporter
closed
9 years ago
2
Dollo model does not parse when BEAGLE is switched on.
#654
GoogleCodeExporter
closed
9 years ago
1
BEAGLE rescaling options, always and delayed, should exhibit identical chains but they don't
#653
GoogleCodeExporter
closed
9 years ago
3
Some conditioning priors need to be evaluated before the data likelihood
#652
GoogleCodeExporter
closed
9 years ago
1
Default Poisson prior for asymmetric BSSVS model of discrete traits is not standard
#651
GoogleCodeExporter
closed
9 years ago
1
java.util.concurrent.ExecutionException when running H5N1_HA_discrete_traits.xml
#650
GoogleCodeExporter
closed
9 years ago
2
Suggest BEAST stops if any of the probabilities go to +Inf
#649
GoogleCodeExporter
closed
9 years ago
1
If you log a multivariate trait for a node to a log file then it is enclosed in curly braces
#648
GoogleCodeExporter
opened
9 years ago
4
Selecting robust counting was not creating the correct XML
#647
GoogleCodeExporter
closed
9 years ago
1
Damaged disk image on OS X Mountain Lion
#646
GoogleCodeExporter
closed
9 years ago
4
Discrete traits were generating ancestral reconstructions irrespective of the Ancestral States settings
#645
GoogleCodeExporter
closed
9 years ago
1
[deleted issue]
#644
GoogleCodeExporter
closed
9 years ago
0
Unable to specify a MRCA node to reconstruct ancestral states
#643
GoogleCodeExporter
closed
9 years ago
0
Inappropriate default values provided for microsatellite model parameters in BEAUti
#642
GoogleCodeExporter
closed
9 years ago
0
BEAUti Tips-dates in Windoz
#641
GoogleCodeExporter
closed
9 years ago
5
GUI error when canceling species-tree analysis
#640
GoogleCodeExporter
closed
9 years ago
2
allow config -Xmx for all beast scripts
#639
GoogleCodeExporter
closed
9 years ago
5
Virus locations and sera locations are improperly collapsed
#638
GoogleCodeExporter
closed
9 years ago
1
birth-death sampling model seems to not work smoothly
#637
GoogleCodeExporter
closed
9 years ago
3
Unlinked codons and state reconstruction in BEAUTi
#636
GoogleCodeExporter
closed
9 years ago
5
*BEAST 'species' attributes are being created outside the <taxon> elements
#635
GoogleCodeExporter
closed
9 years ago
1
Multivariate continuous trait analyses should give variance/covariance matrices and the root estimates by default
#634
GoogleCodeExporter
closed
9 years ago
4
Multivariate continuous trait analyses doesn't respect ancestral state reconstruction choices
#633
GoogleCodeExporter
closed
9 years ago
1
Feature request: BEAUti to be able to fully parse and open BEAUti XML files
#632
GoogleCodeExporter
closed
9 years ago
1
Code generated by BEAUti for substitutions trees doesn't load into BEAST
#631
GoogleCodeExporter
closed
9 years ago
1
Add a progress indicator to Path Sampling
#630
GoogleCodeExporter
closed
9 years ago
1
BEAST doesn't appear to be using multithreading
#629
GoogleCodeExporter
closed
9 years ago
1
Unlinked clock models on multiple partitions fail to run
#628
GoogleCodeExporter
closed
9 years ago
2
Error renaming clock-group
#627
GoogleCodeExporter
closed
9 years ago
1
Trouble unsetting robust counting when partitioning scheme remove
#626
GoogleCodeExporter
closed
9 years ago
2
BEAUti XML invalid for 1 codon-partitioned partition and any 2nd partition
#625
GoogleCodeExporter
opened
9 years ago
2
Check boxes in BEAUti States panel do not line up.
#624
GoogleCodeExporter
closed
9 years ago
1
Logging multiple branch rate models in same tree log is broken
#623
GoogleCodeExporter
closed
9 years ago
4
BEAUti: the "big" updown operator is missing for *BEAST when calibration
#622
GoogleCodeExporter
closed
9 years ago
1
r3896 and r4062 broke Skyride in BEAUti
#621
GoogleCodeExporter
closed
9 years ago
2
BEAUti only allows taxon sets >1 taxa
#620
GoogleCodeExporter
closed
9 years ago
1
BEAUti bug: cannot select a defined taxon set in "Apply to taxon set" at the Tip date sampling
#619
GoogleCodeExporter
closed
9 years ago
4
BEAUti errors in States panel
#618
GoogleCodeExporter
closed
9 years ago
3
BEAUti misnames treeLikelihood ID
#617
GoogleCodeExporter
closed
9 years ago
3
A new bug in BEAST 1.7.1 when importing a nexus-tree in BEAUti
#616
GoogleCodeExporter
closed
9 years ago
3
Multivariate traits generation by BEAUti was broken in the 1.7.1 update.
#615
GoogleCodeExporter
closed
9 years ago
1
Writing Newick user tree in BEAUti doesn't quote taxa with space in the name
#614
GoogleCodeExporter
closed
9 years ago
1
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