This release is compatible with BEAST 2.7. Internally everything should stay the same, although beware that older MASTER XMLs which refer explicitly to BEAST 2 classes may need to be modified to account for the changes in BEAST.

Also, as of this release, the "stand alone" distribution if MASTER is discontinued. (In other words, a working BEAST 2 installation is now required to run MASTER.)

This release addresses a bug that caused BeastTreeFromMaster to ignore taxon sets, if provided.

As always, MASTER-x.y.z.zip is the standalone distribution (no BEAST required), while MASTER.package.vx.y.z.zip is the BEAST package (installable via BEAUti's package manager).

This release is explicitly compatible with the latest version of BEAST.

This release introduces a new class, CompositeLineageEndCondition, which allows multiple
LineageEndConditions to be grouped together in such a way that the composite condition is
met only if all of the constituent conditions are met. This makes it possible to construct end
conditions that are met only if, for example, at least a certain number of lineages for each of
several types exist at a particular time.

Full documentation is provided on the MASTER wiki.

As always, MASTER-x.y.z.zip is the standalone distribution (no BEAST required), while MASTER.package.vx.y.z.zip is the BEAST package (installable via BEAUti's package manager).

The BeastTreeFromMaster simulation type allows one to provide a RealParameter to the input "origin" which is then set to the time before the most recent sample of the simulated tree. Previously, the code which initialized this value was using an approach that had the side-effect of the lower and upper bounds of the initialized RealParameter being set to zero. This made the parameter inoperable, in the sense that any ScaleOperator proposal would be immediately rejected due to violation of the bounds.

This patch fixes this problem.

As always, MASTER-x.y.z.zip is the standalone distribution (no BEAST required), while MASTER.package.vx.y.z.zip is the BEAST package (installable via BEAUti's package manager).

BEAST 2.5 introduces some library version changes, so maintaining compatibility requires this re-release. This realease is not compatible with older versions of BEAST, but doesn't introduce any new features.

As usual, the standalone version is MASTER-A.B.C.zip while the BEAST 2 package (install via BEAUti's package manager) is MASTER.package.vA.B.C.zip.

This is a patch release that includes some helpful error reporting for inheritance simulations. In particular, it produces a helpful notification when the simulation terminates because the reaction rates have dropped to zero and there is no simulation end time (the simulation time effectively reaches infinity).

As usual, the standalone version is MASTER-A.B.C.zip while the BEAST 2 package (install via BEAUti's package manager) is MASTER.package.vA.B.C.zip.

You can now specify an attribute maxConditionRejects of the main simulation types that puts an upper limit on the number of times the simulation will be restarted due to rejection condition. Useful when MASTER is run remotely to avoid wasting computational resources.

This release fixes a bug that causes the LineageSampler to fail with a null pointer exception when a precise number of subpopulation members is specified within a TrajectoryEnsemble simulation.

Download MASTER-5.0.2.zip if you're interested in the stand-alone version. Otherwise, install using BEAUti's package manager.

This release fixes a bug that causes the LineageSampler to fail with a null pointer exception when a precise number of subpopulation members is specified and that subpopulation is empty.

Download MASTER-5.0.1.zip if you're interested in the stand-alone version. Otherwise, install using BEAUti's package manager.