John A. Rhodes

For the last few years, my primary interest has been the mathematical framework underlying phylogenetics, which is roughly defined as the inference of evolutionary trees from biological data such as genetic sequences. Much of my recent work has focused on using algebraic perspectives to understand probabilistic models of sequence evolution.

Publications: A list (with PDFs) of my publications in phylogenetics is here.

Recent talks:

Spitalfields Day, Isaac Netwon Institute, Cambridge, UK, December 2007, Yggdrasil: Reconstructing the Tree of Life -- Phylogenetic Models and Algebra (slides)

Evolution 2007, Christchurch, NZ, June 2007 -- Identifiability of Phylogenetic Models; E.S. Allman, C. Ane, J. Rhodes

Slides of talk
The main result presented in the talk, that GTR+$\Gamma$ is identifiable, is available here. An appendix gives an informal, but detailed, exposition of the gaps in the proof published by Rogers in Sys.Biol., 50(5), 2001, pp. 713--722.

Textbook:

Mathematical Models in Biology
An Introduction

Elizabeth S. Allman and John A. Rhodes, Cambridge University Press, October 2003

MATLAB mfiles and Solution Manual: http://www.cambridge.org/us/catalogue/catalogue.asp?isbn=9780521525862&ss=res
(Note this web address is different from that printed in the text.) Solution manual requires password provided to instructors by CUP. The solution manual will be updated shortly -- the corrected version has a date of Jan.14, 2005 on its cover.

Errata: errata.pdf   (Please e-mail additional errors to j.rhodes@uaf.edu .)

Courses:

Fall 2008

Math/CS 661 Optimization
Textbooks will be
- Nocedal &Wright, Numerical Optimization, 2nd. ed, Springer
- Ferris, Mangasarian, & Wright, Linear Programming with MATLAB, SIAM