Using SplitsTree to Explore Consensus Trees and Networks



Introduction

Note that SplitsTree accepts a range of different types of data (trees, distances between taxa, and characters), which can be supplied in several different formats.

The this guide to using SplitsTree focus on a rather limited set of its functionality
When using SplitsTree in this way, the user will notice that there are many different menus and menu options that are not referred to in this guide. They are encouraged to explore these options and possibilities, but should realise that this may cause the descriptions provided below to no longer be valid.

Getting SplitsTree

SplitsTree is a phylogenetic network viewer and manipulator.

SplitsTree is developed by the same group as Dendroscope. As a result, there are many similarities in the interfaces of the two packages.

The software can be downloaded from this site.

Opening a Multi-Tree NEWICK/PHYLIP Format File

Note that SplitsTree accepts a range of different types of data (trees, distances between taxa, and characters), which can be supplied in several different formats

A. Indicate that you want to open a file using either: B. Select the file to be opened using your operating system's menus
You will be presented with the "Tree names" window - providing a list of the names of the trees contained in the input file - if these names are not assigned in the file, they are simply labeled "t1", "t2", "t3" etc. - this window allows you to change/edit the names of any trees by double-clicking on the names and editing them using the box that then appears
C. Click "Apply" in the "Tree names" window (to accept the names assigned by SplitsTree to each of the trees in the input file)
As the input file contained a set of trees in non-NEXUS format, SplitsTree carries out an appropriate set of default actions/calculations - in this case simply presenting the first tree from the file in displayed as an unrooted tree

SplitsTree Graphical User Interface (GUI)

Main Window

Each file/document opened in SplitsTree is associated with a main window. The main features/components of such a window are shown in the image below.


Processing Pipeline Window

Many/most of the calculations you will perform are controlled/initiated via the "Processing Pipeline" Window - which typically looks similar to the screenshot show below.

At the top of the window are a set of "Blocks", each of which is associated with a set of one or more "Tabs". This guide will focus on using the Method tab of the Trees block.


Calculate a Consensus Tree

  1. Load a set of trees into SplitsTree
  2. Trees->Consensus Tree
  3. In the "Method" tab of the "Trees" block in the "Processing Pipeline" window make sure the following options are selected:
  4. Click "Apply" - the consensus tree you have calculated should then appear in the "Network" tab of the Main Window.

Calculate a Consensus Network

  1. Load a set of trees into SplitsTree
  2. Networks->Consensus Network
  3. In the "Method" tab of the "Trees" block in the "Processing Pipeline" window make sure the following options are selected:
  4. Click "Apply" - the consensus network should appear in the "Network" tab of the Main Window. The length of an edge describes the number of trees in the initial set that contained the split represented by the edge.

Inspect the Tree/Network

When working with a reasonably large set of taxa and trees, you will usually need to view the tree at several different levels of detail to examine the features of interest to you.

The main tools you will use to examine the networks are:
To display the weights associated with all edges/branchs on a tree:

Format the Tree/Network

A very similar set of options are available to adjust the appearance of edges/branches etc. as found in Dendroscope

Author: Aidan Budd
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