The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction. Hill, J. & Davis, K. Biodiversity Data Journal, 2:e1053, Pensoft Publishers, March, 2014.
doi  abstract   bibtex   
Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.
@ARTICLE{Hill2014-bg,
  title     = "{The Supertree Toolkit 2: a new and improved software package
               with a Graphical User Interface for supertree construction}",
  author    = "Hill, Jon and Davis, Katie",
  abstract  = "Building large supertrees involves the collection, storage, and
               processing of thousands of individual phylogenies to create
               large phylogenies with thousands to tens of thousands of taxa.
               Such large phylogenies are useful for macroevolutionary studies,
               comparative biology and in conservation and biodiversity. No
               easy to use and fully integrated software package currently
               exists to carry out this task. Here, we present a new
               Python-based software package that uses well defined XML schema
               to manage both data and metadata. It builds on previous versions
               by 1) including new processing steps, such as Safe Taxonomic
               Reduction, 2) using a user-friendly GUI that guides the user to
               complete at least the minimum information required and includes
               context-sensitive documentation, and 3) a revised storage format
               that integrates both tree- and meta-data into a single file.
               These data can then be manipulated according to a well-defined,
               but flexible, processing pipeline using either the GUI or a
               command-line based tool. Processing steps include standardising
               names, deleting or replacing taxa, ensuring adequate taxonomic
               overlap, ensuring data independence, and safe taxonomic
               reduction. This software has been successfully used to store and
               process data consisting of over 1000 trees ready for analyses
               using standard supertree methods. This software makes large
               supertree creation a much easier task and provides far greater
               flexibility for further work.",
  journal   = "Biodiversity Data Journal",
  publisher = "Pensoft Publishers",
  volume    =  2,
  pages     = "e1053",
  month     =  mar,
  year      =  2014,
  issn      = "1314-2828, 1314-2828",
  doi       = "10.3897/BDJ.2.e1053"
}

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