BEAST2 package DENIM

DENIM can be installed using BEAUTi. Choose File->Manage packages to install, upgrade and uninstall packages. There is documentation inside the package. If you don't know where BEAUTi has installed the package, click on the question mark at the bottom of the Manage packages dialog.

DENIM (Divergence Estimation Notwithstanding ILS and Migration) is still under development, and version 0.3.0 is a beta verion.

Version 0.3.0 of DENIM is available. Requires BEAST 2.4.

Migration Analyser

Migration Analyser is a command line tool for analysing the output of DENIM. MigrationAnalyser.jar. More details are in the DENIM manual.

BEAST2 package STACEY

STACEY can be installed using BEAUTi. Choose File->Manage packages to install, upgrade and uninstall packages. There is documentation inside the package. If you don't know where BEAUTi has installed the package, click on the question mark at the bottom of the Manage packages dialog.

STACEY is described in the paper Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology, 2016. DOI 10.1007/s00285-016-1034-0. Author version. Final published version.

Version 1.2.4 of STACEY is available. Earlier versions are below. Requires BEAST 2.4.

R scripts for making BEAST2 XML files for STACEY containing the simulated data from Olave et al (2014), Syst Biol. This may be useful as a starting point for making BEAST2 XML files for other data.

SpeciesDelimitationAnalyser

speciesDA.jar (15Mb). Jar file containing SpeciesDelimitationAnalyser. (This is basically BEAST1 again, but packaged for convenience.) Run like:

java  -jar speciesDA.jar <SpeciesDelimitationAnalyser arguments> <input file> <output file>
For example:
java -jar speciesDA.jar -burnin 50 -collapseheight 0.00003 -simcutoff 1.0 spptrees.txt clusterings.txt

DISSECT in BEAST1

DISSECT is available in BEAST v1.8.1. The following link is only provided as a fall-back solution in case there is some problem with DISSECT in 1.8.1.

BEAST1DISSECT.jar (15Mb). Jar file containing a version of BEAST1 which includes the DISSECT model. Run like:

java -jar BEAST1DISSECT.jar <BEAST arguments> <BEAST1 XML>

For example:

java -jar BEAST1DISSECT.jar -working -overwrite -window BEAST1DissectExample.xml

Old versions of STACEY

Version 1.2.3 of STACEY is available. Requires BEAST 2.4.

Version 1.2.2 of STACEY is available. Requires BEAST 2.4.

Version 1.2.1 of STACEY is available. Requires BEAST 2.4.

Version 1.2.0 of STACEY is available. Requires BEAST 2.4.

Version 1.1.1 of STACEY is available. It should behave exactly like 1.1.0, when used with the STACEY template. A new template for StarBEAST has been added.

Version 1.1.0 (beta) of STACEY is available. Since it is a beta version, it is not available directly from Beauti. Download the zip file, and see 2.1 in the manual (inside the doc folder) for how to do this. It requires BEAST v2.3, and therefore Java 8. Changes 1.0.5 to 1.1.0:

Version 1.0.5 of STACEY is available. This requires BEAST v2.3, and therefore Java 8. Changes 1.0.4 to 1.0.5:

OLD Version 1.0.4 of STACEY. This requires BEAST v2.3, and therefore Java 8. Changes 1.0.3 to 1.0.4:

OLD Version 1.0.3 of STACEY. This requires BEAST v2.3, and therefore Java 8. Changes 1.0.1 to 1.0.3 (there was no 1.02):

OLD Version 1.0.1 of STACEY. This requires BEAST v2.2, and therefore Java 8. Earlier versions of BEAST and Java will not be supported by STACEY. Changes 0.3.0 to 1.0.1: