Improved facilities for initialising from known trees

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.

Compatibility with BEAST 2.4, slight syntax change

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.

Includes files for short 2 deme tutorial

This release adds an example fasta file h3n2_2deme.fna which is used as the basis for the
short version of the beginner's tutorial.

Resume bug fix.

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.

Added support for ghost demes

As well as some minor bug fixes, this update adds support for demes that are not explicitly sampled. This feature is not yet exposed in the BEAUti interface, but please get in touch (raise an issue!) if you need this sooner rather than later.

Added node type logger

This release includes a new logger (with BEAUti support) that produces trees with type information recorded only at their non-type-change (i.e. coalescent ant sampling) nodes. This is identical to the location tree output of the discrete trait phylogeography package and thus can be analyzed in the same way using TreeAnnotator to produce a summary tree.

Parameter bound bug fix.

This release fixes a bug that was causing lower bounds on population size and rate parameters to be ignored.

BEAUti template improvement.

This minor update removes a superfluous input editor from the BEAUti template.

Fixed alignment issues in BEAUti

This release fixes some minor alignment issues in the BEAUti migration model input editor.

Adds support for human readable types in tree log files.

Previously, multi-type tree log files included type information as integer-valued attributes. With this release, types are labeled using the same strings used in the original type/location trait, improving readability of the output. This means, for instance, that the legend produced by FigTree can contain actual location names rather than "0", "1", "2", etc.