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U(1) × U(1) × U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes
Citation
Bashford, JD and Jarvis, PD and Sumner, JG and Steel, MA, U(1) U(1) U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes, Journal of Physics A-Mathematical and General, 37, (8) pp. L81-L89. ISSN 0305-4470 (2004) [Refereed Article]
DOI: doi:10.1088/0305-4470/37/8/L01
Abstract
An analysis of the Kimura 3ST model of DNA sequence evolution is given on the basis of its continuous Lie symmetries. The rate matrix commutes with a U(1) × U(1) × U(1) phase subgroup of the group G L (4) of 4 ×4 invertible complex matrices acting on a linear space spanned by the four nucleic acid base letters. The diagonal 'branching operator' representing speciation is defined, and shown to intertwine the U(1) × U(1) × U(1) action. Using the intertwining property, a general formula for the probability density on the leaves of a binary tree under the Kimura model is derived, which is shown to be equivalent to established phylogenetic spectral transform methods.
Item Details
| Item Type: | Refereed Article |
|---|---|
| Research Division: | Physical Sciences |
| Research Group: | Other Physical Sciences |
| Research Field: | Physical Sciences not elsewhere classified |
| Objective Division: | Expanding Knowledge |
| Objective Group: | Expanding Knowledge |
| Objective Field: | Expanding Knowledge in the Physical Sciences |
| UTAS Author: | Bashford, JD (Dr James Bashford) |
| UTAS Author: | Jarvis, PD (Dr Peter Jarvis) |
| UTAS Author: | Sumner, JG (Dr Jeremy Sumner) |
| ID Code: | 30825 |
| Year Published: | 2004 |
| Web of Science® Times Cited: | 3 |
| Deposited By: | Physics |
| Deposited On: | 2004-08-01 |
| Last Modified: | 2010-06-10 |
| Downloads: | 0 |
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