PhyRe

Phylogenetic Representativeness is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics, it makes possible to evaluate taxon coverage within a given ingroup. The method relies entirely on taxonomic  information and is based on two ecological indexes (Warwick and Clarke, 1995; Clarke and Warwick, 1998; Warwick and Clarke, 1998; Clarke and Warwick, 2001). A third statistic is the von Euler Index of Imbalance (IE; von Euler, 2001), which gives a rough idea about under- or over-representation of groups within a given sample. The method is extensively illustrated in the paper by Plazzi et al., (2010). A Python-based script suite, called PhyRe, has been developed to implement all analyses. You can download it freely by clicking the links below.

References:

PLAZZI F., FERRUCCI R.R., PASSAMONTI M. (2010) Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. BMC BIOINFORMATICS, 11:209. PDF


 
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