Phylogenetics has gained in public favor for the analysis of DNA sequence data as molecular biology has advanced. Among a number of algorithms for phylogenetics, the fastDNAml is considered to have reasonable computational cost and performance. However, it has a defect that its performance is likely to be significantly affected by the order of taxon addition. In this paper, we propose a genetic...

Phylogenetic analysis may be considered to be a highly reliable and important bioinformatics tool. The importance of phylogenetic analysis lies in its simple manifestation and easy handling of data. The simple tree representation of the evolution makes the phylogenetic analysis easier to comprehend and represent as well. The varied applications of phylogenetics in different fields of biology ma...

The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (clades) in the tree. We extend earlier work to derive exact formulae for the pr...

1. Here, I present a new,multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input ⁄output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and...

Phylogenetic systematics seeks to describe and reconstruct the evolutionary relationships among and between organisms making use of molecular data. This field has become immensely popular in recent years, with the associated computational demands growing in leaps and bounds. Here, we review the progress made in statistical phylogenetics, compare the various methods and highlight the recent tren...