Technical Reference for Creating Tree of Life Pages

by Katja Schulz and David Maddison

The following pages provide instructions on how to create Tree of Life pages using ToL-MacClade. If you are not already familiar with MacClade, you should start with MacClade Basics. If you have used MacClade before, but you are a first-time Tree of Life author, you should refer to the ToL Tutorial for step-by-step instructions on how to put together your first ToL page. If you have mastered the features outlined in the Tutorial, you can refer to the pages about the Sections of Tree of Life pages for comprehensive instructions on how to enter all the information that is relevant to your ToL page into the windows and fields provided by ToL-MacClade.

Introduction to ToL-MacClade

• MacClade Basics
  These pages provide authors who are not familiar with MacClade with a instructions about creating files, entering data, and manipulating trees in MacClade.
  • Working with MacClade data files
    • How to create a new MacClade data file.
    • How to open an existing MacClade data file.
    • How to save a MacClade data file.
    • How to close a MacClade data file.
  • Working with taxa in MacClade
    • How to add taxa in a MacClade data file.
    • How to name taxa in a MacClade data file.
  • Working with trees in MacClade
    • How to create a tree in a MacClade data file.
    • How to move branches on a tree in a MacClade data file.
    • How to create polytomies in a tree in a MacClade data file.
    • How to rotate branches in a tree in a MacClade data file.
• Using ToL-MacClade to create Tree of Life pages
  This page explains how ToL-MacClade uses different types of files in the process of building Tree of Life pages.
• Advanced ToL-MacClade features
  This page explains a couple of the automatic processing features of ToL-MacClade.

Sections of Tree of Life pages

These pages explain how to enter the information associated with different ToL page sections into the windows and fields provided by ToL-MacClade.

• Toolbars
  • Information for the new ToL navigation bar
    • Links to the containing group
    • Links to accessory pages
  • Implementing toolbars during ToL page development
• Title of page
• Title pictures, including figure captions
• Information about authors
• Tree or classification
  • Naming taxa
  • Adding lead text
  • Adding text after the tree or classification
  • Common problems in displaying trees
  • Displaying a classification instead of a tree
  • Labelling internal nodes
  • Assigning ranks
  • Properties of terminal taxa
    • Taxa that are not monophyletic
    • Taxa of uncertain phylogenetic placement (incertae sedis)
    • Extinct taxa
    • Footnotes for terminal taxa
  • Linking descendent pages
• Text sections below the tree: Topics
  • Table of Contents
  • Predefined topics
  • Creating your own topics
  • Topics Manager
  • Entering information for a topic
  • Inserting pictures of trees into text topics
• About this page section, including authors' addresses, acknowledgements, etc.
• Information on the Internet section