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Optimizing Phylogenetic Networks for Circular Split Systems
March/April 2012 (vol. 9 no. 2)
pp. 535-547
ASCII Text
x 
 
Paul Phipps, Sergey Bereg, "Optimizing Phylogenetic Networks for Circular Split Systems," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 535-547, March/April, 2012.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2011.109,
author = {Paul Phipps and Sergey Bereg},
title = {Optimizing Phylogenetic Networks for Circular Split Systems},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {9},
number = {2},
issn = {1545-5963},
year = {2012},
pages = {535-547},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.109},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Optimizing Phylogenetic Networks for Circular Split Systems
IS - 2
SN - 1545-5963
SP535
EP547
EPD - 535-547
A1 - Paul Phipps,
A1 - Sergey Bereg,
PY - 2012
KW - Computational biology
KW - phylogenetic network
KW - minimizing faces
KW - split network
KW - network optimization.
VL - 9
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Paul Phipps, University of Texas at Dallas, Richardson
Sergey Bereg, University of Texas at Dallas, Richardson
We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix.

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Index Terms:
Computational biology, phylogenetic network, minimizing faces, split network, network optimization.
Citation:
Paul Phipps, Sergey Bereg, "Optimizing Phylogenetic Networks for Circular Split Systems," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 535-547, March-April 2012, doi:10.1109/TCBB.2011.109
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