Simulated annealing in the search for phylogenetic trees
View/ Open
Barker2000_FULL.pdf (12.78Mb)
Date
18/07/2000Author
Barker, Daniel
Metadata
Abstract
I investigate use of the simulated annealing heuristic to seek phylogenetic trees
judged optimal according to the principle of parsimony. I begin by looking into the
central data structure in phylogenetic research, the tree. I discuss why it is usually
necessary to employ a heuristic, rather than an exact method, when seeking
parsimonious trees. I summarise different heuristic approaches. I explain how to use
the program LVB, written to use simulated annealing in the search for parsimonious
trees. I use LVB, with different combinations of values for parameters controlling the
annealing search, to re-analyse two DNA sequence data matrices, one of 50 objects
and one of 365 objects. Equations to estimate suitable control parameters, on the
basis of desired run time and quality of result, are fitted to data obtained by these
analyses. Future directions of research are discussed.