TREEMAP 1.0

User's Guide

by

Roderic D. M. Page, Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow

Contents


1. What is TreeMap?

2. Getting started

3. Overview of program

4. Managing Reconstructions

5. Finding the best reconstruction(s)

6. Randomisation tests

7. Managing TreeMap files

References


1. What is TREEMAP?


TREEMAP is designed as a simple tool for visually comparing host and parasite phylogenies: you can view the host and parasite trees, interactively create reconstructions of the history of the host-parasite association, perform randomisation tests of tree similarity, and (if you have branch length information such as might be obtained from DNA sequence data) compare branch lengths in the two trees.

I should emphasise that TREEMAP is an experimental program for comparing host and parasite trees. It started out as a test bed for my research, and is not a finished product. It is offered free and on an "as-is" basis to anyone interested in host-parasite cospeciation. It runs on Apple® Macintosh®'s and under Microsoft® Windows™.

1.1 Copyright notice


Copyright © 1995 Roderic D. M. Page.

Permission to use and distribute this software and its documentation for any purpose is hereby granted without fee, provided the above copyright notice, author statement and this permission notice appear in all copies of this software and related documentation.

THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

IN NO EVENT SHALL THE AUTHOR, THE DEPARTMENT OF ZOOLOGY OR THE UNIVERSITY OF OXFORD BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

1.2 Contacting the author


If you have bug reports, comments or suggestions, please contact me at this address:

Roderic D. M. Page, Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, university of Glasgow, Glasgow G12 8QQ, United Kingdom

email: r.page@bio.gla.ac.uk

fax: +44 141 330 5971

tel: +44 141 330 6993

1.3 Acknowledgements


TREEMAP would not have been ported to the Macintosh without Eddie Holmes and Paul Harvey (University of Oxford) lending me their PowerBooks. Andrew Rambaut offer advice on things Macintosh. Writing the program was made easier by using ideas from the National Center for Biotechnology's VIBRANT library written by Jonathon Kans. TREEMAP is written in C++ and compiled with Turbo C++ 3.1 (Windows) and Symantec C++ 7.0 (Macintosh).