Bioarchaeology of the Near East, 10:69-73 (2016)

Technical Note: A GNU Octave function for Smith's Mean Measure of Divergence

Andreas Bertsatos*, Maria-Eleni Chovalopoulou
Department of Animal and Human Physiology,
National and Kapodistrian University of Athens,
Panepistimioupolis 157 72, Athens, Greece
email: abertsatos@biol.uoa.gr (corresponding author)

Abstract: The present paper introduces a function written in GNU Octave language for calculating Smith's Mean Measure of Divergence (MMD). The function uses by default the Freeman and Tukey angular transformation but also provides an optional choice for Anscombe's transformation. The Freeman and Tukey correction term is used in both cases. The function calculates the distance and variance matrices of MMD for an arbitrary number of groups (populations) of samples and trait frequencies. The generated matrices are returned in the Phylip format for direct use with tree construction tools.

Key words: GNU Octave language; Smith's MMD; distance matrix; non-metric traits

Received 15 November 2016; accepted 14 January 2017; published online 14 January 2017.

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