dbabox/beast-mcmc

Issues

• Tracer cannot handle different number of log states and tree state for BayesianSkylineDialog

  #272 opened 9 years ago by GoogleCodeExporter
  1

• BEASTParserDoc is unable to generate Wiki format

  #270 opened 9 years ago by GoogleCodeExporter
  2

• correct the link of “BEAUti website”

  #271 opened 9 years ago by GoogleCodeExporter
  1

• BEAUti: prior distribution error message "find incorrect number format"

  #268 opened 9 years ago by GoogleCodeExporter
  1

• duplicate id in BEAST Parser Library html

  #269 opened 9 years ago by GoogleCodeExporter
  3

• BEAUTi: The user should *always* be allowed to fix the rates if they want

  #267 opened 9 years ago by GoogleCodeExporter
  2

• BEAST getting slower

  #265 opened 9 years ago by GoogleCodeExporter
  1

• BEAST: tree prior expansion + growth not working

  #266 opened 9 years ago by GoogleCodeExporter
  1

• BEAST ARG bug

  #263 opened 9 years ago by GoogleCodeExporter
  3

• ImportException: Number format error for <treeTraceAnalysis ...

  #264 opened 9 years ago by GoogleCodeExporter
  1

• wrong XML of testCataclysmCoalescent.xml

  #262 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi: Mac OS MCMC panel problem

  #259 opened 9 years ago by GoogleCodeExporter
  1

• BEAUTi: correct English

  #260 opened 9 years ago by GoogleCodeExporter
  1

• Error parsing <traceAnalysis> element with id null

  #261 opened 9 years ago by GoogleCodeExporter
  1

• BEAUTi: Binary data and multiple partitions does not generate the siteModel correctly.

  #257 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi: Crash when trying to generate an XML file with the covarion.

  #258 opened 9 years ago by GoogleCodeExporter
  1

• Turn off parser WARNINGs by default for released version

  #255 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi: Add comment in XML "skyride.logPopSize is log unit unlike other popSize"

  #256 opened 9 years ago by GoogleCodeExporter
  1

• BEAUTi add a pop-up box to check the default priors when click Generate BEAST file

  #253 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi generate XML button should be disable after all data partition removed

  #254 opened 9 years ago by GoogleCodeExporter
  1

• Opening 'examples/starBEAST/g10.xml' gives null pointer exception

  #251 opened 9 years ago by GoogleCodeExporter
  2

• Need to be able to add calibration info on species divergences in starBEAST

  #252 opened 9 years ago by GoogleCodeExporter
  1

• GMRF Skyride - "skyride.popSize" and "skyride.precision" stuck on starting values, "gmrfBlockUpdateOperator" changes are never accepted

  #249 opened 9 years ago by GoogleCodeExporter
  5

• BEAUTi: wrong alignment blocks for multi-gene when choosing "create empty alignment"

  #250 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi exception (*BEAST) when linking some same taxa for a tree model by given different taxa in total

  #248 opened 9 years ago by GoogleCodeExporter
  4

• BEAUTi: weak HKY-like Dirichlet prior for GTR relative rates

  #246 opened 9 years ago by GoogleCodeExporter
  1

• BEAUTi: wrong XML in frequecies choosing EMPIRICAL binary COVARION model

  #247 opened 9 years ago by GoogleCodeExporter
  1

• URGENT: Default prior review

  #244 opened 9 years ago by GoogleCodeExporter
  3

• *beast log files returns infinity for posterior and likelihood and a constant prior at aprox 22 million generations

  #245 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi: create a check box to choose useAmbiguities in treeLikelihood for binary data

  #242 opened 9 years ago by GoogleCodeExporter
  1

• create a beast-core-trace.jar library to peel Tracer out of the BEAST

  #243 opened 9 years ago by GoogleCodeExporter
  2

• BEAUTi: useAmbiguities of treeLikelihood should be default as true for binay Covarion

  #240 opened 9 years ago by GoogleCodeExporter
  1

• BEAUTi: operator subtreeSlide size should not be INF

  #241 opened 9 years ago by GoogleCodeExporter
  3

• BEAUTi: taxon set not handling multi-tree partition

  #237 opened 9 years ago by GoogleCodeExporter
  2

• Naming of 'patterns' when only 1 partition

  #238 opened 9 years ago by GoogleCodeExporter
  1

• Ctrl-A in BEAUTi data panel

  #239 opened 9 years ago by GoogleCodeExporter
  1

• Unlinked DiscretizedBranchRates for multiple loci have the wrong number of dimensions

  #235 opened 9 years ago by GoogleCodeExporter
  4

• dr.evomodel.operators.TraitGibbsOperator is duplicated with parsers in either release_parser.properties or BeastParser.java

  #236 opened 9 years ago by GoogleCodeExporter
  1

• Make the dreaded "The initial posterior is zero" error a bit more friendly to debug

  #234 opened 9 years ago by GoogleCodeExporter
  3

• Delay the start of the performance measurement until after full evaluation.

  #231 opened 9 years ago by GoogleCodeExporter
  1

• Mac (Windows?) version of BEAST closes console on error

  #232 opened 9 years ago by GoogleCodeExporter
  1

• Attribute operatorAnalaysis in mcmc is not working in BEAST

  #233 opened 9 years ago by GoogleCodeExporter
  1

• Another failure of testing framework

  #229 opened 9 years ago by GoogleCodeExporter
  1

• Add beast.css for BEASTParserDoc

  #230 opened 9 years ago by GoogleCodeExporter
  3

• LogCombiner mishandles trees with attributes

  #228 opened 9 years ago by GoogleCodeExporter
  5

• The parsers in release_parsers.properties need to be updated

  #226 opened 9 years ago by GoogleCodeExporter
  1

• Fix BeastDoc to generate tag doc for BEAST users

  #227 opened 9 years ago by GoogleCodeExporter
  1

• Set the 'operator analysis' file name as an attribute in MCMC element

  #223 opened 9 years ago by GoogleCodeExporter
  2

• Need to refactory dr.evomodel.arg.ARGModel, which has 4471 lines

  #224 opened 9 years ago by GoogleCodeExporter
  0

• TreePartitionCoalescent is not existing

  #225 opened 9 years ago by GoogleCodeExporter
  1