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2014 ; ä (2
): e1053
Nephropedia Template TP
gab.com Text
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English Wikipedia
The Supertree Toolkit 2: a new and improved software package with a Graphical
User Interface for supertree construction
#MMPMID24891820
Hill J
; Davis KE
Biodivers Data J
2014[]; ä (2
): e1053
PMID24891820
show ga
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.