Protocol

Bioinformatics for DNA Sequence Analysis

Volume 537 of the series Methods in Molecular Biology pp 139-161

Date:

Trees from Trees: Construction of Phylogenetic Supertrees Using Clann

  • Christopher J. CreeveyAffiliated withEMBL Heidelberg
  • , James O. McInerneyAffiliated withDepartment of Biology, National University of Ireland Maynooth

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Abstract

Supertree methods combine multiple phylogenetic trees to produce the overall best “supertree.” They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down problems thought to be computationally intractable. Some of the longest standing phylogenetic conundrums are now being brought to light using supertree approaches. We describe the most widely used supertree methods implemented in the software program “clann” and provide a step by step tutorial for investigating phylogenetic information and reconstructing the best supertree. Clann is freely available for Windows, Mac and Unix/Linux operating systems under the GNU public licence at http://​bioinf.​nuim.​ie/​software/​clann.

Key words

Supertree software phylogenetic reconstruction phylogeny congruency test phylogenetic signal detection