A recent version of the manual is also available in Media:.PDF format.
Introduction / Overview of GenGIS
Purpose
GenGIS is an application that is designed to integrate
Platforms
System requirements
Citing GenGIS
Where to go for help
Installation
Getting the Release Version
Adding the Python Console
Adding R
Developer Version – building from source code
Input data
Input data ordering
Maps
Supported formats
Projections
Data sources and GDAL
Typical limits on map size
Location File
Required fields
Location data – Lat / Long vs. UTM
Sequence File
Required fields
Other fields
Phylogenetic trees
File formats
Constraints / relationship with sequences
The Environment
The map environment
Map pane
Minimap
Getting around in GenGIS
Control elements
Hotkeys
Console input
Mouse
Shortcut buttons
Interacting with sample sites
Working with Layers
Adding and removing
Active / inactive
wx Elements
Graphical analysis tools in GenGIS
Basic data visualizations
Pie charts
..?
2D phylogenetic trees
Defining axes
Manipulation
3D phylogenetic trees
The Python console and API functions
What you can do with the console
Accessing sample and sequence data
Capturing results
RPy and analyzing data
Installing R modules
Accessing sample data as tables in R
Capturing output from R
Implemented API functions (e.g. Mike's invocation of R charts)
Writing your own API functions
