Projects

Report on Direct-to-Consumer Genetic Testing

Phylogenetic Trees created with three programs that determine the degree of relatedness between organisms by aligning their genetic sequences and creating a confidence interval (1.00 being certain) for how closely they are aligned.

Phylogeny.fr provides a tool called “Robust Phylogenetic Analysis for the Non-Specialist” that aggregates multiple tools into a “one-click” analysis.

The scientists who created this tool are credited below:

Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed)

The analysis can also be done stepwise. The CIPRES Science Gateway is a powerful tool that makes the computational resources necessary to do multiple sequence alignments available to scientists through the CIPRES Portal. Depending on the needs of the project it offers alignment through bootstrapping and maximum likelihood searches as well as a hybrid of the two.

Miller, M.A., Pfeiffer, W., and Schwartz, T. (2010) “Creating the CIPRES Science Gateway for inference of large phylogenetic trees” in Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010, New Orleans, LA pp 1 – 8.

Dendroscope is a piece of tree-generating and viewing software that takes aligned sequences and turns them into beautiful and meaningful phylogenies.

D.H Huson, D.C Richter, C. Rausch, T. Dezulian, M. Franz and R. Rupp. Dendroscope: An interactive viewer for large phylogenetic trees, BMC Bioinformatics. 2007 Nov 22;8(1):460

FigTree is a similar tool to Dendroscope, it turns alignment data into figures for publication.

http://tree.bio.ed.ac.uk/software/figtree/

 

Tree of Life and RDP

Deciphering Alleles with Promethease

More ggplot2 Graphing

Graphing with ggplot2

Object Types and SNP Data in R

My First Ever R Lab