Evidence of Multiple Maximum Likelihood Points
227. B. B. Zhou, M. Tarawneh, D. Chu, P. Wang, C. Wang, A. Zomaya and
R. P. Brent,
Evidence of multiple maximum likelihood points for a phylogenetic
Proc. Sixth IEEE Symposium on Bioinformatics and Bioengineering
(BIBE06), Arlington, Virginia, Oct 2006, 193-197.
An interesting and important, but largely ignored question associated
with the ML method is whether there exists a single maximum
likelihood point for a given phylogenetic tree.
Mike Steel [Syst. Biol. 43 (1994), 560-564]
presented a simple analytical results to argue that the ML point is
not unique. However, so far his view has attracted little attention.
Though many researchers believe that multiple maximum likelihood points
may exist for certain phylogenetic trees, most existing phylogenetic
construction programs only produce a single best tree under the ML
criterion and in practice many researchers still use only the ML values
to make a judgment on the quality of different trees for a given problem.
In this paper we present some experimental results from a large number
of synthetic test data sets and show that it is quite common that certain
incorrect trees can have likelihood values at least as large as that of
the correct tree. A significant implication of this is that even if we
are able to find a globally optimal tree under the maximum
likelihood criterion, this tree is not necessarily the correct
phylogenetic tree. In this paper we also show that our newly developed
algorithm can perform much better in terms of accuracy than well-known
algorithms such as FASTDNAML and PHYML, by constructing
more than one tree for a given problem.
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