(The RadCon Manual v1.1.3)

The RadCon Manual

About The RadCon Manual

netscape document icon This manual was written by Joseph L. Thorley and Mark Wilkinson to document the RadCon program.

If you need to cite the documentation we suggest 

        J.L. Thorley and M. Wilkinson. 2007. The RadCon Manual v. 1.1.3. http:/bmnh.org/systematics/RadCon/ 

About The RadCon Program

netscape document icon RadCon is a free MacOS(Classic) program for manipulating and analysing phylogenetic trees

It was written by Joseph L. Thorley and Roderic D. M. Page

It can be downloaded free from the RadCon Home Page.

If you use this version of RadCon to analyze trees for publication, the citation is:
J.L. Thorley and R.D.M. Page 2000. RadCon: Phylogenetic tree comparison and consensus. Bioinformatics. 16. 486-487.

Table of Contents

How to Read This Manual

This manual is written in HTML (HyperText Markup Language) - the language of web pages and should be viewed using an approriate web browser. Pictures form a large part of this manual and the browser should be set to view pictures. The appearance of text of different types is set using Style Sheets and these should be enabled in the browser. In addition some simple JavaScript is used by a few pages to provide an interactive explanation of various terms. JavaScript should be enabled in the browser.

Please note that due to time constraints we have only tested this manual for viewing using Internet Explorer 4 and Netscape Navigator 4. If you are using earlier versions of these browsers we strongly suggest you upgrade - they are free!

This manual was not written to be read cover-to-cover! This manual is meant to be a resource for the user to refer to whenever information about RadCon is required. The user should, starting from the Table of Contents, follow the appropriate links until the appropriate section is reached. Links to other sections should be followed if additional clarity is required.

For ease of use all 'active' text in this manual is underlined. Internal text links - which provide links to pages of this manual when double-clicked - appear thus before visiting and thus after visiting. External text links - which provide links to pages on the internet - appear thus before visiting and thus after visiting. Rollover text - which provides interactive effects when the cursor is moved over it - appears thus.

Introduction to RadCon

This section provides a very brief overview of some of the most interesting features of RadCon - don't be fooled into thinking that this is all RadCon does!

Before telling you a little about what RadCon does we ought to tell you what it doesn't! RadCon is a program for manipulating and analysing phylogenetic trees. RadCon does not input phylogenetic data such as DNA sequences or morphological character states - it only deals with trees. RadCon does not reconstruct phylogenies - it must be given the trees it deals with. RadCon does not map characters onto trees - it only deals with tree structure.

So RadCon is a program for dealing with trees. How does it differ from other tree programs? A key difference, between RadCon and most other tree programs, is RadCon's ability to handle trees with non-identical sets of leaves. A difference that permits the production of strict reduced consensus trees and facilitates the consruction of supertrees .

As well as the strict reduced consensus method, which may output multiple consensus trees, RadCon provides the user with two other strict (sensu Wilkinson 1994) consensus methods - the Adams and the strict component consensus. The choice of consensus tree has been considered an insoluble by some authors. This is not the case in RadCon as the user can use Cladistic Information Content (CIC) to identify the single most informative strict consensus tree and make an informed choice.

The ultimate goal of phylogenetics is the reconstruction of the tree of life! However practical and theoretical problems limit individual studies to tiny parts of this tree. leaves . The user can measure the extent to which trees in the same set agree about the position of individual leaves (Positional Congruence) and measure the certainty surrounding the position of each leaf in a set of bootstrap trees (Leaf Stability).

The bootstrap is not the only method for measuring the stability of phylogenetic hypotheses. Another favourite is the Decay Index. The Leaf Stability (Decay Index) and Double Decay Analysis options enable the user to assess the stability of individual leaves and explore less inclusive, but better supported, hypotheses than full splits, respectively, using this measure.


Legal Agreement

The RadCon program and documentation are provided as is, without guarantee of maintenance or support, and without warranty. The copyright holders are not liable for any damages which may result in any manner from the use of this software.

System Requirements

RadCon requires a Power Macintosh running MacOS 7.5 or later.

The font file PAUP Font file should be installed in the Fonts folder in the System Folder. The PAUP Font file is distributed with RadCon with permission from Dave Swofford.

The Interface

RadCon is designed to be user-friendly. The user is provided with a graphical interface that includes drop-down menus, various windows and balloon help.

Getting Help

This manual was written to be a comprehensive guide to using RadCon.

RadCon also provides the user with Balloon Help, a source of immediately available information about various commands, options and features.

If neither of these sources provides the required information questions can be sent to Joe Thorley or Mark Wilkinson.

Return to the Table of Contents.

This page is maintained by Mark Wilkinson and was last modified February 15, 2007