In this paper, we introduce the HashRF(p, q) algorithm for computing RF matrices of large binary, evolutionary tree collections. The novelty of our algorithm is that it can be used to compute arbitrarilysized (p × q) RF matrices without running into physical memory limitations. In this paper, we explore the performance of our HashRF(p, q) approach on 20,000 and 33,306 biological trees of 150 ta...

colibacillosis is of the most common infectious bacterial diseases of poultry.a total of 170 escherichia coli isolates obtained from broiler and layer flocks implicated with colibacillosis between 2011 and 2014 were subjected to phylogenetic analysis. among 150 e. coli isolates from typical lesions of local and systemic colibacillosis, 54 (31.8%), 37 (21.7%), 36 (21.2%) and 43 (25.3%) isolates ...

Phylogenetics is the study of the origin, development, and death of a taxon. It is a useful tool, for example, in the conservation of species. This chapter is an introduction to phylogenetics from the perspective of plant molecular biologists, using a case study on Saururaceae. Based on analysis using integrated data from DNA sequences and morphology, we also draw a surprising conclusion that S...

IV. Methods of Analysis of Molecular Data A. Phylogenetic Analysis 1. Tree-Building Methods 2. Statistical Methods for Testing the Reliability of a Tree 3. Other Methods B. Phylogenetics versus Population Genetics V. Application of Molecular Methods in Amphibian Systematics A. Determination and Identification of Species and Species Hybrids B. Molecular Phylogeny of Living Amphibians 1. The Phyl...

1. Modern phylogenetic comparative biology uses data from the relationships between species (phylogeny) combined with comparative information for phenotypic traits to draw model-based statistical inferences about the evolutionary past. Recent years have seen phylogeny methods for evolutionary inference become central in the study of organic evolution. 2. Here, I present two different graphical ...

UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage...

We investigate uniqueness issues that arise in l∞-optimization to linear spaces and Bergman fans of matroids. For linear spaces, we give a polyhedral decomposition of R based on the dimension of the set of l∞-nearest neighbors. This implies that the l∞-nearest neighbor in a linear space is unique if and only if the underlying matroid is uniform. For Bergman fans of matroids, we show that the se...

Here we briefly present an overview of our research in two topics: 1. Experimental and theoretical aspects of phylogeny inference and 2. Development of software for molecular phylogenetic inference and phylogenetic genome