Minor release with JBLAS v1.2.5.

This release includes an upgraded version of JBLAS which should hopefully resolve some issues people have been having running MTT on m1+ macs.

Compatibility with BEAST 2.7.

This release adds compatibility for BEAST 2.7. Thanks to @jordandouglas and @walterxie for their work on this port!

Minor bug fix

This release fixes an error in the mouse-over documentation given for the adjustTipHeights input to MultiTypeTreeFromNewick and MultiTypeTreeFromNewick.

Brought up-to-date with BEAST 2.6.0

This release makes MultiTypeTree explicitly compatible with BEAST 2.6.0.

Major release: GUI changes and compatibility with BEAST 2.5

As well as bringing compatibility with BEAST 2.5, this major release fundamentally changes how types are named and how those names are tracked internally. From a user perspective, the new features this has enabled include:

• sensible inference of the required dimensionality of migration rate and population size matrices,
• ability to specify "ghost" demes from within BEAUti,
• ability to specify global scale factors for migration rates and population sizes, meaning that the magnitude of individual elements of the migration rate matrices and population size vectors can be treated as relative, helping with prior specification - particularly when the relative rates/sizes are known,
• a much friendlier BEAUti experience overall.

WARNING: this release is not backwards compatible with existing MTT XML files.

Fix for serialization bug

This release addresses an issue that arose due to a recent change in the way that BEAST2 generates a serialized representation of the MCMC state for later resumption of the chain. This change caused MTT's existing serialization code to produce corrupted coloured tree representations that could not be used for chain resumption.

With this update, it is once again possible to resume MTT analyses.

MTT version 7 (pre-release)

This is a pre-release for v7. It fundamentally changes how types are named and how those names are tracked internally. From a user perspective, the new features this has enabled include:

1. sensible inference of the required dimensionality of migration rate and population size matrices,
2. ability to specify "ghost" demes from within BEAUti,
3. ability to specify global scale factors for migration rates and population sizes, meaning that the magnitude of individual elements of the migration rate matrices and population size vectors can be treated as relative, helping with prior specification - particularly when the relative rates/sizes are known,
4. a much friendlier BEAUti experience overall.

Currently this release is not backwards compatible with existing MTT XML files. I'm hoping that I'll be able to address this before the full release.

As always, comments are welcome.

GUI stability improvements

This release introduces a couple of important improvements to the BEAUti interface:

1. It is no longer possible within this interface to set up XMLs in which the number of types/demes specified in the model is fewer than the number of unique types/demes in the data.

2. The portion of the Priors panel which allows editing the starting population and migration rate matrix parameters now gives a number of useful hints about what the different elements mean. For example, the columns corresponding to source locations (backward in time). The correspondence between location names and the migration matrix and population size vector indices is also now shown.

Suppressed checkValidity in BEAUti.

This is an antiquated option that isn't generally useful for users, so hiding it reduces unnecessary complexity.

Support for logging lenghs of type-associated lineages

This release adds a new logger (enabled in the BEAUti-generated XML by default) which records total length of the tree associated with each deme/type.