Related papers: A Simple Characterization of the Minimal Obstructi…
Perfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam's Razor such…
We study the perfect phylogeny problem and establish a generalization of the four gamete condition (also called the Splits Equivalence Theorem) for sequences over three state characters. Our main result is that a set of input sequences over…
Phylogenetic trees represent evolutionary relationships and can be uniquely defined by sets of finite-state biological characteristics. Despite prior work showing that sufficiently large trees can be determined by $r$-state character sets,…
Perfect phylogeny consisting of determining the compatibility of a set of characters is known to be NP-complete. We propose in this article a conjecture on the necessary and sufficient conditions of compatibility: Given a set $\mathcal{C}$…
The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary)…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
We show that for any two values $\alpha, \beta >0 $ for which $\alpha+\beta>1$ then there is a value $N$ so that for all $n \geq N$ the following holds. For any binary phylogenetic tree $T$ on $n$ leaves there is a set of $\lfloor n^\alpha…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
We study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function $f(r)$ such that, for any set $C$ of $r$-state characters, $C$ is compatible if and only…
Techniques are developed for creating new and general language families of only semilinear languages, and for showing families only contain semilinear languages. It is shown that for language families L that are semilinear full trios, the…