admixture  - Code to prepare data for admixture analysis

ancestral  - Generating Ancestral (and genome distance) tables

excfg      - Example configuration files

geo        - Geo-referencing

inbreeding - Calculating inbreeding

meta       - Data curation and meta-data

phasing    - Pipeline taking ped and hapmap data through
             beagle and generating XPEHH and iHS formatted files

scripts    - Standalone scripts

support    - Miscelaneous support code

web        - Web software


CONFIGURATION

Configuration of the system is done by 2 configuration files:

~/.megacfg - with information about the location of the databases

local.cfg - specific configuration file (most of the times NOT NEEDED).