The genealogical sorting index (*gsi*) quantifies the degree of exclusive ancestry of labeled groups on a rooted genealogy (Cummings, Neel and Shaw 2008). The statistic is useful for testing the differentiation of species and populations or subpopulations. The probability of an observed genealogical sorting index value is estimated by permutation.

The algorithm for calculating the genealogical sorting index was written in R, a statistical programming environment. We provide two ways to use the program. A parallel computing resource for running the analysis is available via a web interface (http://www.genealogicalsorting.org/) for users interested in quickly calculating the genealogical sorting index and performing permutation tests on phylogenetic trees. It will eventually be available as an open source package on the Comprehensive R Archive Network (http://cran.r-project.org/); in the meantime, the R package is available for download.

**Input Format:**

Two input files are needed –

- rooted tree file in NEXUS or Newick format containing only representatives for groups you wish to analyze (e.g., no outgroup)
- class (group) assignment file in plain text

**Sample files**

- simple_trees
- simple_assignments

Additional sample files are available. Alternatively, the assignment file can be created using the web interface.

**Instructions for All:**

To begin analysis, go to the web site: http://www.genealogicalsorting.org/.