CompEvol/beast2

Issues

• BEAST 2 version on bioconda lags behind a bit

  #1167 opened 2 months ago by m-d-grunnill
  0

• Package manager GUI hangs when 'Install/Upgrade' is done on package installed by hand

  #1166 opened 2 months ago by rbouckaert
  0

• BEAST 2.7.7 is not launched after update

  #1165 opened 2 months ago by trilisser
  3

• No clean way to add external package repositories from the command line

  #1163 opened 2 months ago by tgvaughan
  0

• java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.isRoot()" because "<parameter1>" is null

  #1162 opened 3 months ago by liamxg
  0

• Add case to Tree.adjustTreeNodeHeights method to accommodate zero-length branches

  #1161 opened 3 months ago by jjmccollum
  0

• When is a node's nodeNr ever greater than the root's nodeNr?

  #1160 opened 3 months ago by jacklo225
  1

• Request a feature to use "version_file" in AppLauncher

  #1158 opened 3 months ago by walterxie
  2

• Resuming from a state file does not update parameter dimensiom

  #1159 opened 3 months ago by jordandouglas
  1

• Running into errors when following "WRITING A BEAST 2.7 PACKAGE" guide

  #1128 opened a year ago by jacklo225
  8

• Class (orc.consoperators.UcldScalerOperator) could not be found

  #1157 opened 4 months ago by Chonghao98
  4

• Generate xml file in linux command line

  #1156 opened 5 months ago by Chonghao98
  2

• Remove jars when updating packages

  #1155 opened 5 months ago by rbouckaert
  1

• .xml.state not found

  #1146 opened 7 months ago by kesiaeds
  5

• Feature request: partial monophyly constraints

  #1153 opened 5 months ago by seraklop
  6

• Treeannotator not going to 100%

  #1154 opened 5 months ago by asad-869
  1

• Randomizer per thread for deterministic behaviour when using threads

  #1141 opened 5 months ago by rbouckaert
  1

• Prep for v2.7.7 release

  #1152 opened 5 months ago by rbouckaert
  0

• no main manifest attribute on newer release

  #1151 opened 6 months ago by xk42
  0

• Make Alignment a StateNode

  #1150 opened 6 months ago by rbouckaert
  0

• Hiccups with preparing package for testing

  #1149 opened 6 months ago by jacklo225
  1

• BEAST2: fatal error has been detected by the Java Runtime Environment

  #1132 opened a year ago by Rutaiwan
  3

• Likelihood incorrectly calculated error

  #1148 opened 7 months ago by jkimsis
  5

• Resume problem for monophyletic

  #1147 opened 7 months ago by walterxie
  5

• error in parsing xml with no prior manual editing

  #1145 opened 8 months ago by ptitle
  2

• BEAUti error importing alignment

  #1144 opened 8 months ago by dmsoong
  1

• TreeAnnotator does not respond to TargetTreeType in GUI

  #1143 opened 8 months ago by rbouckaert
  0

• Clarification about Trees and StateNodeInitialiser

  #1142 opened 8 months ago by jacklo225
  4

• BEAST.base installation

  #1140 opened 9 months ago by NRuizVargas
  0

• BEAST 2.7.6 not launching on Mac

  #1139 opened 9 months ago by kbhoehn
  0

• Add CCD package to list of recommended packages

  #1138 opened 9 months ago by rbouckaert
  4

• BEAST apps don't launch on Windows 10

  #1137 opened 10 months ago by ms609
  4

• AdaptableOperatorSampler should ignore operators with zero weight

  #1136 opened 10 months ago by rbouckaert
  0

• java.lang.Error: randomChoiceUnnormalized falls through -- negative components in input distribution?

  #1135 opened a year ago by Sikandar37
  2

• How can I find out number of patterns and number of partitions from my input file without running Beast2?

  #1134 opened a year ago by mzhuangsdsc
  6

• Robustify package manager

  #1133 opened a year ago by rbouckaert
  0

• Prep for v2.7.6 release

  #1131 opened a year ago by rbouckaert
  0

• beauti doesn't format html in package descriptions.

  #1121 opened a year ago by SimonGreenhill
  0

• Parameter does not restore properly after dimension change

  #1130 opened a year ago by rbouckaert
  0

• AdaptableOperatorSampler should have a try catch around calling the tree metrix

  #1129 opened a year ago by jordandouglas
  0

• Warning: Duplicate cpuset controllers detected

  #1127 opened a year ago by MordorianGuy
  7

• BEAUti does not set a specified Clock.rate of `ClusterTree`.

  #1124 opened a year ago by MordorianGuy
  5

• BactrianUpDownOperator modifies the wrong index when elementWise is true

  #1126 opened a year ago by bjoelle
  1

• Should `dataInput` of `ClusterTree` be named "taxa"?

  #1123 opened a year ago by MordorianGuy
  2

• Input setStringValue for non-numerical list inputs

  #1125 opened a year ago by rbouckaert
  0

• Tree.printTranslate not robust

  #1122 opened a year ago by rbouckaert
  1

• About BEAST2 run error

  #1119 opened a year ago by bseonghyeon
  4

• RPNCalculator argnames input

  #1118 opened a year ago by rbouckaert
  0

• Prep for v2.7.5 release

  #1116 opened a year ago by rbouckaert
  0

• Generalization of root and tip distributions as RootDistribution and TipDistribution

  #1115 opened a year ago by kche309
  0