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In order to seamlessly identify the links between various DNA sequences on a broad scale, DNA sequencing is a crucial tool. But there is still more potential for advancement in sequencing quality. A highly well-liked method for determining sequence ...

The ${\mathcal{R}}^{+-}{\mathcal{F}}^{+-}$Consistency problem is a basic problem related to the construction of phylogenetic trees. Its input is two sets $R^{+}$ and $R^{-}$ of resolved triplets and two sets $F^{+}$ and $F^{-}$ of unresolved triplets (also known as fan triplets). The objective of ...${}^{}{}^{}$${}^{}{}^{}$${\mathcal{}}^{}$${\mathcal{}}^{}{\mathcal{}}^{}$${\mathcal{}}^{}$${\mathcal{}}^{}{\mathcal{}}^{}$

In bioinformatics, accurate phylogenetic tree construction from a genome sequence is one of the biggest concerns nowadays. Getting the optimal k-mer for this construction is the main concern of this work. In the early day’s alignment-based approach for ...

In many clades in the Tree of Life, nucleotide substitution rates and base frequencies are hypothesized to have changed as genome evolution unfolded over time. Rigorous testing of this hypothesis relies on accurate phylogenetic reconstruction under ...

We give a counterexample to the conjecture of Martin and Thatte that two balanced rooted binary leaf-labeled trees on $n$ leaves have a maximum agreement subtree (MAST) of size at least $n^{\frac{1}{2}}$. In particular, we show that for any $c>0$, there ...

Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, “tree-based” phylogenetic networks, which are defined by a spanning tree called a “subdivision tree” that ...

Cancer evolution is often modeled by clonal trees (whose nodes are labeled by multiple somatic mutations) or mutation trees (where nodes are labeled by single somatic mutations). Clonal trees are generated from sequence data with different computational ...

Multiple sequence alignment (MSA) is a basic step in many analyses in bioinformatics, including predicting the structure and function of proteins, orthology prediction and estimating phylogenies. The objective of MSA is to infer the homology among the ...

In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where $k$ is the tree bisection and reconnection distance between the two trees. Here ...

Various computational and statistical approaches have been proposed to uncover the mutational patterns of rapidly evolving influenza viral genes. A problem that draws much attention is to identify pairs of sites that potentially co-mutate to contribute ...

We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all ultrametrics. The ${CAT}(0)$ metric of Billera--Holmes--Vogtman arises from the theory of orthant spaces. ...

The rapidly growing amount of ancient human genetic data enables the tracking of the spread of human populations over time. However, several challenges that need new solutions in order to most effectively mine the available data. We introduce an ...

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the neighborhoods ...

Semple and Steel (2002) showed that if ${\cal T}$ is a phylogenetic $X$-tree and ${\cal C}$ is a collection of $r$-state characters that defines ${\cal T}$, then $|{\cal C}|\ge \lceil(n-3)/(r-1)\rceil$, where $n=|X|$. In this paper, we show that, provided $...

Phylogenetic analysis is commonly used to analyze genetic sequence data from fungal communities, while ordination and clustering techniques commonly are used to analyze sequence data from bacterial communities. However, few studies have attempted to ...

Given two rooted phylogenetic trees on the same set of taxa $X$, the Maximum Agreement Forest (maf) problem asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic Agreement Forest (...

Many of the stochastic models used in inference of phylogenetic trees from biological sequence data have polynomial parameterization maps. The image of such a map---the collection of joint distributions for all parameter choices---forms the model space. ...

In various research fields a common task is to summarize the information shared by a collection of objects and to find a consensus of them. In many scenarios, the object items for which a consensus needs to be determined are rankings, and the process is ...

In this paper, we introduce a new evolutionary tree algorithm that is based on common mutation similarity matrices instead of distance matrices.

Abstract The Robinson-Foulds RF distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster MC distance, which can be regarded as a ...