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- Mareike Fischer, Mike Steel
- Journal of theoretical biology
- 2009

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary relationship accurately depends on the model of sequence evolution, the substitution rate, divergence times and the method… (More)

- Mareike Fischer, Leo van Iersel, Steven Kelk, Céline Scornavacca
- SIAM J. Discrete Math.
- 2015

Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as Maximum Parsimony need to be modified in order to be applicable to networks. In this paper, we discuss two… (More)

- Mareike Fischer, Bhalchandra D Thatte
- Journal of theoretical biology
- 2009

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the… (More)

- Mareike Fischer
- 2012

In a recent study, Steel and Sanderson defined and characterized phylogenetically decisive sets of taxon sets. A set is called phylogenetically decisive if regardless of the trees chosen for each of its taxon sets, as long as these trees are compatible with one another, their supertree is always unique. This implies that the sampled taxon sets always lead… (More)

- Steven Kelk, Mareike Fischer
- ArXiv
- 2014

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the… (More)

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under… (More)

- Mareike Fischer, Bhalchandra Thatte
- Bulletin of mathematical biology
- 2010

Tuffley and Steel (Bull. Math. Biol. 59:581-607, 1997) proved that maximum likelihood and maximum parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since. We show that small changes to the model assumptions suffice to… (More)

- Olivier Boes, Mareike Fischer, Steven Kelk
- IEEE/ACM Transactions on Computational Biology…
- 2017

Given two phylogenetic trees on the same set of taxa <inline-formula><tex-math notation="LaTeX">$X$ </tex-math><alternatives><inline-graphic xlink:href="kelk-ieq1-2543727.gif"/></alternatives></inline-formula>, the maximum parsimony distance <inline-formula><tex-math notation="LaTeX">$d_\mathrm{MP}$</tex-math> <alternatives><inline-graphic… (More)

- Steven Kelk, Mareike Fischer, Vincent Moulton, Taoyang Wu
- Theor. Comput. Sci.
- 2016

In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in tree inference, we recently introduced the maximum parsimony (MP) distance, which enjoys various attractive properties… (More)

- Mareike Fischer
- ArXiv
- 2011

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequenc-ing is still a time-consuming and costly process. Therefore, decision criteria would be desirable to decide a priori which data might contribute new… (More)