A New Quartet-based Phylogeny Reconstruction Algorithm
223. B. B. Zhou, M. Tarawneh, D. Chu, P. Wang, C. Wang, A. Y. Zomaya and
R. P. Brent, On a new quartet-based phylogeny reconstruction algorithm,
Proceedings 2006 International Conference on Bioinformatics and
Computational Biology (BIOCOMP06), Las Vegas, USA, June 2006, 87-93.
Recently we developed a new quarted-based algorithm for phylogenetic
analysis . This algorithm constructs a
limited number of trees for a given set of DNA or protein sequences and
the initial experimental results show that the probability for the correct
tree to be included in this small set of trees is very high.
In this paper we further extend the idea. We first discuss a revision to
the original algorithm to reduce the number of trees generated, while
keeping the high probability for the correct tree to be included.
We then deal with the issue of how to retrieve the correct tree from
the set of generated trees. Our current approach is to calculate the
likelihood values of these trees and select a few which have the highest
likelihood values. Though the experimental results are comparable to
those obtained from currently popular ML-based algorithms, we find
that it is 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 truly globally optimal tree
under the maximum likelihood criterion, this tree is not necessarily the
correct phylogenetic tree.
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