| Genealogical Sorting Index |
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The genealogical sorting index (gsi), which quantifies the degree of exclusive ancestry of labeled groups on a rooted genealogy
(Cummings, Neel and Shaw 2008 in press). The statistic is useful for testing the differentiation of species and populations or subpopulations. The significance of an observed genealogical sorting index value is measured with permutation testing.
The algorithm for calculating the genealogical sorting index was written in R, a statistical programming environment. We provide two ways to use the program. It will soon be available as an open source package on The Comprehensive R Archive Network (http://cran.r-project.org/). 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.
Input data file formats
Two input files are needed -
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rooted tree file in NEXUS or Newick format containing only representatives for groups you wish to analyze (e.g., no outgroup)
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class (group) assignment file in plain text
Sample files
Additional sample files are available. Alternatively the assignment file can be created on via the web interface.
Instructions
To begin analysis, go to the web site: http://www.genealogicalsorting.org/.
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