Jianxin Wang — Page 5

arXiv2014

Algorithms for Maximum Agreement Forest of Multiple General Trees

The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work about the Maf problem are mainly on two binary phylogenetic trees or two general (i.e., binary and non-binary) phylogenetic trees. In this paper, we study the more general version of the problem: the Maf problem on multiple general phylogenetic trees. We present a parameterized algorithm of running time $O(3^k n^2m)$ and a 3-approximation algorithm for the Maf problem on multiple rooted general phylogenetic trees, and a parameterized algorithm of running time $O(4^k n^2m)$ and a 4-approximation algorithm for the Maf problem on multiple unrooted general phylogenetic trees. We also implement the parameterized algorithm and approximation algorithm for the Maf problem on multiple rooted general phylogenetic trees, and test them on simulated data and biological data.

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arXiv2008

A Parameterized Perspective on $P_2$-Packings

}We study (vertex-disjoint) $P_2$-packings in graphs under a parameterized perspective. Starting from a maximal $P_2$-packing $\p$ of size $j$ we use extremal arguments for determining how many vertices of $\p$ appear in some $P_2$-packing of size $(j+1)$. We basically can 'reuse' $2.5j$ vertices. We also present a kernelization algorithm that gives a kernel of size bounded by $7k$. With these two results we build an algorithm which constructs a $P_2$-packing of size $k$ in time $\Oh^*(2.482^{3k})$.

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