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>
java -jar BEAST1DISSECT.jar -working -overwrite -window BEAST1DissectExample.xml
STACEY can be installed using BEAUTi.
File->Manage packages to install, upgrade and uninstall packages.
It seems necessary to restart BEAUTi before STACEY will work with BEAUTi.
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 1.2.3 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):
BirthDeathCollapseModel.initAndValidate()for collapse weight and relative death rate. (The checks failed if the parameters were not estimated, I don't know why.)
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:
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.
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