Related papers: Towards the fixed parameter tractability of constr…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…
We provide a number of algorithmic results for the following family of problems: For a given binary m\times n matrix A and integer k, decide whether there is a "simple" binary matrix B which differs from A in at most k entries. For an…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
In this paper, we focus on the prediction phase of a random forest and study the problem of representing a bag of decision trees using a smaller bag of decision trees, where we only consider binary decision problems on the binary domain and…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Mathematical modeling is a standard approach to solve many real-world problems and {\em diversity} of solutions is an important issue, emerging in applying solutions obtained from mathematical models to real-world problems. Many studies…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted binary phylogenetic trees on taxon set X in time (6r)^r.poly(n), where n=|X|. The novelty of this approach is that it avoids the…
Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…