Microbiology Commons^™

Phylometrics: A Pipeline For Inferring Phylogenetic Trees From A Sequence Relationship Network Perspective, Samuel A. Smits, Cleber C. Ouverney

Faculty Publications, Biological Sciences

Background
Comparative sequence analysis of the 16S rRNA gene is frequently used to characterize the microbial diversity of environmental samples. However, sequence similarities do not always imply functional or evolutionary relatedness due to many factors, including unequal rates of change and convergence. Thus, relying on top BLASTN hits for phylogenetic studies may misrepresent the diversity of these constituents. Furthermore, attempts to circumvent this issue by including a large number of BLASTN hits per sequence in one tree to explore their relatedness presents other problems. For instance, the multiple sequence alignment will be poor and computationally costly if not relying on …

Jsphylosvg: A Javascript Library For Visualizing Interactive And Vector-Based Phylogenetic Trees On The Web, Samuel A. Smits, Cleber C. Ouverney

Faculty Publications, Biological Sciences

Background
Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees.

Methods/Principal Findings
We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is …