LPhyBEAST v1.2.1

Require LPhy 1.6.1 or a higher version, and BEAST 2.7.7.

Significant changes:

• Operator for supporting negative values #156

Bug fix and new feature:

• replace FastRelaxedClockLogNormal to ORC #151
• Extension loading issue while running LPhyBEAST 1.1.0 via cmd #152
• Update README.md with updated command and hyperlink #157
• Will removing the E = rmTaxa(names=1:3, alignment=D); from jcCoalescent.lphy has any further effect on generated XML and future analysis? #158
• More controls in Logger and Loggable #161
• treelikelihood should set useAmbuguities=true as default #166

LPhyBEAST v1.2.0

Require LPhy 1.6.0 or a higher version, and BEAST 2.7.7.

From version 1.2, LPhyBEASTExt is moved to here.

Significant changes:

• Change to setup IntelliJ as Maven project #140
• Update BEAST dependencies to 2.7.7 #148

Bug fix and new feature:

• It should exclude Value's type not the Value itself #135
• use getExcludedGenerator first #136
• Model misspecification test #137
• Add UpDownOperator to PopulationFunction #139
• LocalClockToBeast dependency setting #145
• Merge LPhyBeast-Ext to this repo #147

LPhyBEAST v1.1.0

Require LPhy 1.5.0 or a higher version, and BEAST 2.7.6.

Significant changes:

• Update standard operators to Bactrian operators used in BEAST 2.7.x #109
• migration to lphy 1.5 #112

Bug fix:

• Command line args do not behaviour properly when using relative paths #104
• Recognise LPhy Macro in LPhyBEAST #125

An example of command line to change the constants in the given lphy script containing Macro:

YOUR_BEAST/bin/lphybeast -o Yule/20/yule-n20.xml -l 50000000 -le 1000 -r 100 -D "n=20;L=600" Yule.lphy

LPhyBEAST v1.0.5

Require LPhy 1.4.5 or a higher version, and BEAST 2.7.5.

Bug fix:

• null Exception when not using Macro #126

New command line argument to change the constants in the given lphy script, this will search the line having the same variable id as the parsed variables from the script and replace its value. The script must be the original lphy script, no Macro language.

YOUR_BEAST/bin/lphybeast -o Yule/20/yule-n20.xml -l 50000000 -le 1000 -r 100 -d "n=20;L=600" Yule.lphy

This will update the values n=20 and L=600. The provided lphy script has n=10 and L=300.

LPhyBEAST v1.0.4

Require LPhy 1.4.5 or a higher version, and BEAST 2.7.5.

Download lphybeast or lphybeast.bat from LPhyBEAST v1.0.2 release.

Install "lphybeast" from BEAST 2 "Package Manager".

New command line argument to change the constants in the given lphy script:

YOUR_BEAST/bin/lphybeast -o Yule/20/yule-n20.xml -l 50000000 -le 1000 -r 100 -d "n=20;L=600" Yule.lphy

This will update the values n=20 and L=600. The provided lphy script has n=10 and L=300.

Bug fix and new features:

• WilsonBalding and WideExchange should be more like size^0.2 #122
• change constants in command line arguments #124

LPhyBEAST v1.0.3

Require LPhy 1.4.5 or a higher version, and BEAST 2.7.5.

Download lphybeast or lphybeast.bat from LPhyBEAST v1.0.2 release.

Install "lphybeast" from BEAST 2 "Package Manager". To download the launcher, click on the "Assets" below to expand it, and then select the appropriate download link. Details in https://linguaphylo.github.io/setup/.
See also https://github.com/LinguaPhylo/LPhyBeastExt.

Critical change:

• Re-design TreeOperatorStrategy #119

Bug fix:

• Add lphy script to the top of XML #94
• add a "logEvery" command line option #116
• BirthDeathSerialSampling error #118

LPhyBEAST v1.0.2

Require LPhy 1.4.3 or a higher version, and BEAST 2.7.5.

Install "lphybeast" from BEAST 2 "Package Manager". To download the launcher, click on the "Assets" below to expand it, and then select the appropriate download link. Details in https://linguaphylo.github.io/setup/.
See also https://github.com/LinguaPhylo/LPhyBeastExt.

Critical change:

• lphybeast script finds $LPHY_LIB #86, which updates the lphybeast launcher to remove the limitation of having to install LPhy under the BEAST 2 folder.

Bug fix:

• Windows logging issue #113

LPhyBEAST v1.0.1

Require LPhy 1.4.2, and BEAST 2.7.4. See also https://github.com/LinguaPhylo/LPhyBeastExt.

Install "lphybeast" from BEAST 2 "Package Manager". Details in https://linguaphylo.github.io/setup/

Bug fixes and new features:

• Add tests for lphy example scripts to convert into BEAST 2 XMLs #78
• Should use getAsRealParameter() #90
• simulate alignment from the 2nd lphy script #96
• BEAST new loader not working in GitHub #106
• LPhyBEAST release dependency description incorrect #108

LPhyBEAST v1.0.0

Require Java 17, LPhy 1.4.1, and BEAST 2.7.4. See also https://github.com/LinguaPhylo/LPhyBeastExt.

Install "lphybeast" from BEAST 2 "Package Manager". Details in https://linguaphylo.github.io/setup/

Run LPhyBEAST from a terminal using the command line:

$BEAST_FOLDER/bin/lphybeast $LPHY_FOLDER/tutorials/RSV2.lphy

Bug fixes and new features:

• phyloCTMC.getQ() => phyloCTMC.getQValue() #91
• Create LPhyBeastConfig to contain all settings #95
• Use LPhyBeastConfig to contain all settings #97
• Migrate to beast 2.7 #98
• NoClassDefFoundError: groovy.lang.Closure #101
• Log all intermediate alignments #105

LPhyBEAST v0.4.2

Require Java 17, LPhy 1.3.1, and BEAST 2.6.7. See also https://github.com/LinguaPhylo/LPhyBeastExt.

Install "lphybeast" from BEAST 2 "Package Manager". Details in https://linguaphylo.github.io/setup/

Run LPhyBEAST from a terminal using the command line:

$BEAST_FOLDER/bin/lphybeast $LPHY_FOLDER/tutorials/RSV2.lphy

Bug fixes and new features:

• DPG TreeWithTraitLogger #84
• auto set pre-burnin is skipped #85
• script lphybeast finds the lphy lib #86
• update lphy to 1.3.1 and fix h5n1 tutorial LinguaPhylo/linguaPhylo#221