Related papers: Phylogenetic Networks
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…
Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters, but some morphological features may not necessarily…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…
A network is a typical expressive form of representing complex systems in terms of vertices and links, in which the pattern of interactions amongst components of the network is intricate. The network can be static that does not change over…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…