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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.

Assets 3

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.

@tgvaughan tgvaughan released this Apr 13, 2017 · 13 commits to master since this release

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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.

@tgvaughan tgvaughan released this Mar 24, 2017 · 29 commits to master since this release

Assets 3

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.

@tgvaughan tgvaughan released this Jun 29, 2016 · 37 commits to master since this release

Assets 3

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

Assets 3

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.

Assets 3

This release improves the MultiTypeTreeFromNewick class used for initialising chains from known typed trees. It also includes an additional class MultiTypeTreeFromUntypedNewick which initialises the untyped portion of the typed tree using a Newick string and simulates type changes down this using MTT's uniformization algorithm.

Instructions for using these classes and doing fixed tree analyses can be found on the wiki.

@tgvaughan tgvaughan released this Mar 7, 2016 · 50 commits to master since this release

Assets 3

This release provides compatibility with BEAST 2.4, which implements several API changes requiring a complete re-release. This release is not compatible with earlier versions of BEAST. In addition, this release renames the MigrationModel class to SCMigrationModel, paving the way for other models besides the structured coalescent.

@tgvaughan tgvaughan released this Jan 21, 2016

Assets 3

This release fixes a bug due to code left over from the previous incarnation of TreeParser. That version used nexus comments such as [type=1] to specify tree node metadata. This was contrary to the standard set by BEAST 1 and other parts of BEAST 2 which uses instead comments of the form [&type=1]. The updated TreeParser fixes this, but caused a bug in MultiTypeTree because of its reliance on the old form. This release fixes that bug.

In case you're wondering, yes - this should have been picked up by the serialization/deserialization unit tests. That it wasn't is also a bug in those tests.