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Open Access Methodology article

Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

Federico Plazzi1*, Ronald R Ferrucci2 and Marco Passamonti1

Author Affiliations

1 Department of "Biologia Evoluzionistica Sperimentale", University of Bologna, Via Selmi, 3 - 40126 Bologna, Italy

2 Department of Biology and Evolution, University of Ferrara, Via Borsari, 46 - 44100 Ferrara, Italy

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BMC Bioinformatics 2010, 11:209 doi:10.1186/1471-2105-11-209

Published: 27 April 2010

Additional files

Additional file 1:

PhyRe scripts and documentation. Three Python scripts constitute the PhyRe package. PhyRe script itself performs main analyses presented in this paper: AvTD, VarTD, IE, and funnel plots parameters are computed by this script. PhyloSample generates shuffled master lists, whereas PhyloAnalysis repeats PhyRe tasks across all newly-generated master lists. All scripts have been tested under Python 2.5.4. PhyRe documentation (doc.pdf) and eight sample files referring to datasets used in the paper to validate the method [19-22] are also enclosed.

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Additional file 2:

Real and simulated data from bivalve data set. Real and simulated data from bivalves data set follow Millard [23] reference taxonomy. Table shows the composition of our real and simulated samples of bivalves. Taxonomy is reported for each genus; a plus "+" sign indicates the presence of that genus in that sample.

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