Population subgrouping analysis

Hi all:

I have a population consisting of 1000 different individual plant varieties collected from different latitudes (i.e. the geographic coordinates specifying the north-south positions on surface of Earth). We have generated close to 3000 molecular data points for each of the individual plants. The data point for each molecular marker is either "0" or "1". I'm interested in a statistical analysis program/software that can divide the 1000 individual plant varieties into subgroups/subpopulations based on the molecular data. I'm also interested in identifying individual plant varieties that are outliers when the population gets sub-divided into subpopulations/subgroups. Your assistance would be highly appreciated!