We propose the following simple stochastic model for phylogenetic trees. New types are born and die according to a birth and death chain. At each birth we associate a fitness to the new type sampled from a fixed distribution. At each death the type with the smallest fitness is killed. We show that if the birth (i.e. mutation) rate is subcritical, we obtain a phylogenetic tree consistent with an...

Scientists often wish to use the information contained in the DNA sequences of a collection of organisms, or taxa, to infer the evolutionary relationships among those taxa. These evolutionary relationships are generally represented by a labeled binary tree, called a phylogenetic tree. The phylogeny reconstruction problem is computationally di cult because the number of possible solutions increa...

A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus--but often incomplete--sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic amb...

Motivation: Phylogenetic tree construction is a complex yet important problem in the field of bioinformatics. Once constructed, a phylogenetic or evolutionary tree can lend insight into the evolution of different species. The issue is that for a large number of species the problem grows to a computational complexity that is not easily solved. For this reason, new methods are being researched an...

classify specified organisms taxonomically, determine the origins of proteinencoding genes, and infer how proteins function based on their conserved sequence motifs. Typically, phylogenic analysis involves two steps: constructing a phylogenetic tree or network based on the given biosequences and deriving biological information from the tree or network. Many computational methods have been devel...

A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, Phylogenetic Tree Construction package. The package supports four well-known algorithms, Unweighted Pair Group Method using Arithmetic average, Neighbor Joining, Fitch Margoliash, and Maximum Parsimony.

We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.