Optimizing Phylogenetic Networks for Circular Split Systemsby Paul Phipps and Sergey Bereg
Abstract:
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.
@article{pb-opn-12, 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}, issn = {1545-5963}, year = {2012}, pages = {535-547}, url = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.109}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, } |