This is a list of changes in GXNA version 2.0 (compared to version 1.x). See
the web documentation for more details.

New features:
- added mouse interaction network mouse.gra
- added several array annotation files
- output now in HTML format, drawings show interaction type
- several phenotypes can be compared (ANOVA F statistics)
- moderated (empirical Bayes shrinkage) test statistics can be used
- Metropolis style randomized search can be used
- better default values for command line arguments

Technical changes:
- annotation file extension changed from .map to .ann to avoid
browser download problems
- GXNA also reads arguments from file named defaults.txt (if it exists)
- phenotypes can be any string; there is no longer an "ignore" phenotype
- scoreType 2 and 3 now correspond to F statistics, but these are set
automatically if multiple phenotypes are present; in most cases you do
not need to set scoreType
- new arguments -iterations and -kMet control Metropolis search
- option -graphDir is now named -outputDir, and -summaryFile no longer
exists (it is more or less replaced by -resultsFile)
- the output format is now unified for all types of searches
- several output files are now written: .arg contains program arguments,
.res has detailed results, .html has the HTML output, and for each top
network there is a .txt summary file, .dot graph file, and possibly a
.svg image file