Using ToL-MacClade

We recommend that new Tree of Life authors skip the section on Using ToL-MacClade and let ToL staff create their pages for them. New tools for creating and revising ToL pages will be available soon, and authors can then learn the new system which will be much more user-friendly than ToL-MacClade. If you are a new ToL author who is not yet familiar with ToL-MacClade, please refer to the page on Preparing Text and Figures for Others to Compose for instructions on how to get your materials incorporated into the Tree of Life.

Tree of Life authors who want to create their own HTML files have to do so using the special Tree of Life version of MacClade.MacClade lets you arrange taxa in a phylogenetic tree which can then be analyzed and manipulated in many different ways. The special Tree of Life version of MacClade uses this tree along with information entered into a series of windows and boxes to write a file in HTML format. HTML (Hypertext Markup Language) is the language used to give instructions to World Wide Web browsers to compose pages with text, pictures, active buttons, and so on. Authors who use ToL-MacClade will not have to understand the details of this language, but some minimal knowledge is needed in some places. Fortunately, the language is very simple, and below we provide detailed instructions on how to enter the relevant information for a Tree of Life page.

In the new database version of the Tree of Life, the ToL pages are no longer created directly by ToL-MacClade; instead, pages are assembled from the database by a server-side program. Eventually, this new architecture will be associated with a matching set of new data entry tools. While these tools are still under development, we will continue to use ToL-MacClade files to store information about the content and format of Tree of Life pages; however, instead of using ToL-MacClade itself to create the HTML files directly, we now use the ToL-MacClade data files to convert and import information into the ToL database.

Acquiring ToL-MacClade.

This page contains instruction on how to download the Tree of Life version of MacClade.

Tutorial.

Recommended for first-time authors. This is a tutorial leading you step-by-step through the creation of a collection of Tree of Life pages using ToL-MacClade.

Technical Reference for using ToL-MacClade to build Tree of Life pages.

Recommended after you have learned some basics from the Tutorial section. This is a detailed description of building Tree of Life pages, including all the gory details.

Frequently Asked Questions.

This page contains answers to some of the questions we are frequently asked about using ToL-MacClade for Tree of Life pages.

All the HTML you will likely need to know.

Recommended after you have learned some basics from the Tutorial section. This describes some of the few HTML codes you may need to learn to make your pages look better.

 

Warning

In using ToL-MacClade to create Tree of Life pages, there are two primary files involved: the MacClade file (NEXUS file), which stores all of the information you have entered in MacClade's specialized editors, and the Tree of Life page (HTML file) that ToL-MacClade creates. This Tree of Life page is a text file written in HTML code. In order to be able to take advantage of MacClade's automated updating features (including the automatic integration of pages into the new ToL database), authors have to do all necessary editing and revising ONLY in the ToL-MacClade data file (NEXUS file), i.e., the associated HTML file should never be edited by hand. In the past, some authors have used MacClade to create the Tree of Life page, and then have made changes to the Tree of Life page directly, by opening the page up in a word processor or HTML editor. Please be warned that pages edited in this way are not database-compatible.