1. Introduction

1.1. What is the STK?

The Supertree Tool Kit (STK) is software for collecting, curating, storing and processing data ready for inclusion in supertree analyses. It does not build supertrees, however, it does include a number of functions to get the data ready for running a supertree analysis. This includes standardising nomenclature and taxonomy, ensuring adequate taxonomic overlap and creating a matrix. These functions can be used together as a data processing pipeline or independently as stand-alone options for data processing.

1.2. What does it do?

  • Import bibliographic files to create a dataset
  • Import trees created in most software packages
  • Export your data to common formats (Nexus, Newick, Hennig)
  • Allow you to summarise your data
  • Swap and delete taxa easily
  • Create a matrix from your data
  • Manage your data graphically
  • Ensure data independence
  • Ensure adequate taxonomic overlap
  • Replace non-monophyletic taxa correctly
  • Perform Safe Taxonomic Reduction
  • Some post-processing of supertrees (e.g. pruning taxa)

1.3. What does it not do?

  • Make supertrees

1.4. About this document

This document is the main manual for the software. Included in the software is context-relevant help embedded in the GUI, which is complementary to the manual. This manual will help you install and use the software, but it will still take experience to know which functions are appropriate for your dataset. In addition to this, many of the functions will require human input e.g. making decisions on how to deal with non-independent data or choosing an appropriate taxonomy.

1.5. The processing pipeline

The idea behind the STK is to create a processing pipeline that is robust, error-free, repeatable and easy. A dataset is created by importing bibliographic data and trees, the STK functions are then used to process these data. Each stage in the pipeline creates a new file, with a history of the previous steps embedded. This way it is easy to undo steps and come back to your data later and understand how it was derived.

Warning

This new file does still need to be saved with a new file name, if you “save as” under the previous saved file you will over-write your previous hard work so be aware!

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2. Getting started

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