Hill, Jon orcid.org/0000-0003-1340-4373 and Davis, Katie (2014) The Supertree Toolkit 2:a new and improved software package with a Graphical User Interface for supertree construction. Biodiversity Data Journal. e1053. ISSN 1314-2828
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © Authors. This content is made available by the publisher under a Creative Commons CC BY Licence |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Environment and Geography (York) |
Depositing User: | Pure (York) |
Date Deposited: | 07 Dec 2015 13:45 |
Last Modified: | 21 Jan 2025 17:17 |
Published Version: | https://doi.org/10.3897/BDJ.2.e1053 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.3897/BDJ.2.e1053 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:84569 |