pre release for v2

upadates for version 2.0.0

includes time varying rates for version 2 pre release, also adds simulator for SIR models

Bug fixes in the reheight machinery

fixes a bug in the tip reheight machinery that leads to the taxon not being found in the different parts of the reheight tools. This was likely introduced in v2.7 and causes runs to not start

Fixes missing scalefactor issue in the template

v1.0.3

adds lib folder

fixes antlr error

Fixes the antlr version issue that exists since porting to beast 2.7

Bug fix in beauti connector

fixes issue in beauti connector from porting where the operators on the segment trees are not removed from the xml

Beast 2.7 version of CoalRe

Beast 2.7 release for CoalRe

Bug fix: robustly handle differently-ordered alignments.

This release fixes an oversight that caused CoalRe to implicitly assume that sequences appeared in exactly the same order in every segment-specific alignment.

Proper initialisation for BEAUti-generated analyses.

Previous BEAUti-generated analyses didn't explicitly initialise the segment trees, meaning that they were initially inconsistent with the starting network. Provided the analysis actually ran, this shouldn't have caused any real problem, but it was potentially the source of difficulties in edge cases.

This release provides a fix for that problem.

Upgrade version of feast library used.

This release updates the feast library dependency, but includes no other changes.

Added network summary app.

With this release, the summary app should be available from the BEAST applauncher utility.