The GenGIS Manual

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A recent version of the manual is also available in Media:.PDF format.


Introduction / Overview of GenGIS



System requirements

Citing GenGIS

Where to go for help


Getting the Release Version

Adding the Python Console

Adding R

Developer Version – building from source code

Input data

Input data ordering


Supported formats


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


Getting around in GenGIS

Control elements


Console input


Menu options

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


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