The changes here are all for the beta releases at the moment. As I roll out new stable releases, I'll add a change log for those as well. In case you're interested, stable release 1.7 is equivalent to beta release 1.7.2.

Version 1.7.2

  • Fixed minor bugs parsing unusual Phylip-format files and reporting errors in Nexus files
  • Updated compilation instructions for Ubuntu users

Version 1.7.1

  • Fixed map themes for Windows

Version 1.7

  • Added an option to show/hide sequence labels in networks (makes for tidier figures)
  • Added a "how to cite" dialog
  • Fixed an issue with the documentation ("help contents") on Windows
  • Fixed AMOVA output ("%variation" entries are now percentages)
  • Fixed TCS bug that caused an error message "Progress is not a percentage" to appear and network inference to fail.

Version 1.6

  • Added a population group dialog to allow users to specify groups for nested AMOVA
  • Implemented nested AMOVA
  • AMOVA output format is now similar to that of Arlequin
  • Fixed several bugs (notably saving/loading of edge lengths and several issues that caused PopART to crash while reading some NEXUS files)

Version 1.5

  • Implemented great circle distance clustering of geotagged sequences

Version 1.4

  • Support for Geotagged sequences
  • Support for importing traits or geotags from a tab-, space-, or comma-delimited table
  • Saving and opening networks

Version 1.3

  • Added map interface

Version 1.2

  • Added options to change the default node size and view mutations along edges in three different ways
  • Ancestral Parsimony networks now use edges sampled from ancestral reconstructions on MP trees rather than a minimum spanning network between sampled ancestral sequences
  • The Tight Span Walker algorithm has been changed somewhat, and should work with more datasets
  • Fixed various bugs, including parsing of Nexus files with quotes around command values, e.g., gap="-", and a bug where if "Open File" was cancelled, an existing open file would still be closed

Version 1.1

  • Added support for NEXUS with mid-sequence line breaks (e.g., exported by Seaview)
  • Added support for old-style Mac line breaks (e.g., saved by PAUP* running on Mac Classic)
  • Improved progress bars
  • Sequences now load faster
  • Graph drawing is slightly faster
  • Redraw network now lets you specify how many iterations of the spring embedder to perform (more iterations means slower, but nicer drawings)
  • Fixed bug that only allowed logging to existing files
  • Fixed bug that affected mixed case sequence files
  • Fixed "5 sample" size (radius, rather than area, was 5x the 1 sample radius.It's now 10 samples so that text will fit)
  • Fixed bug in ancestral parsimony where sequence nodes were duplicated