Michael S. Taylor

Southeast Missouri State University

Analyses and Systematics

PAUP Phylogenetic Analysis Using Parsiony (*and other methods), by David Swofford, is essential software for any scientist performing phylogenetic analyses, employing parsimony, likelihood and distance methodology. Available for Mac, Windows and unix platforms. MrBayes MrBayes by John P. Huelsenbeck and Fredrik Ronquist is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
Phylogenetic Analysis by Maximum Likelihood, by Ziheng Yang, is a free set of useful programs for performing phylogenetic analyses on DNA and Protein sequence data. Available for free for Mac and Windows-based computers, or as ANSI C source code. Phylogenetic Software Phylogenetic Software list maintained by Joe Felsenstein. If the software you need isn't included here, then it may not exist.
Arlequin Arlequin, by Laurent Excoffier and colleagues, is essential software for population genetics data analyses. Written in java so portable across a variety of computer platforms. DNAsp DnaSP Software, by Julio Rozas and Ricardo Rozas, can estimate several measures of DNA sequence variation within and between populations, as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.
NCBI National Center for Biotechnology Information is a foundation of essential tools and links for every scientist. Hosted by the National Library of Medicine and the National Institutes of Health. NCBI NCBI Taxonomy Homepage has a taxonomic database and variety of useful taxonomic links.
Ryan Gregory's Animal Genome Size Database is a comprehensive catalogue of animal genome size data. Fishbase FishBase is a comprehensive taxonomic database and more for fishes of the world.
Plate Reconstruction Plate Tectonic Reconstruction: Reconstruct the land masses of yesteryear. Create a Map Create a Map: Excellent site for generating custom vector maps based on longitude and latitude.
Primer3 picks primers from your DNA sequence based on conditions you specify. Webcutter Webcutter identifies restriction enzyme sites in your sequence data.


Dive Deep Dive Deep Underwater Photography: Stunning underwater photography, including many photos of gobies. Dive Deep Extreme Dive Deep Extreme: Companion site to Dive Deep.
Goby Frontiers Goby Frontiers: Photographs of gobies, primarily from Pacific and Indian oceans. Gobiidae.com Gobioid Research Institute: Information on the Gobioidea of the Americas, the eastern Atlantic, and parts of the Indo-Pacific.
Biolum Logo The Bioluminescence Web Page, hosted by the University of California at Santa Barbara, gathers and organizes information about organisms that glow in the marine dark. HBOI Bioluminescence The HBOI Bioluminescence web site, hosted by Dr. Edie Widder, has an excellent introduction to marine bioluminescence.
Porifera Learn more about one of the most basic metazoans with this Introduction to Porifera, hosted by the Museum of Paleontology at the University of California, Berkeley. Flatworms Marine Flatworms of the World is a new site that is building a gallery of gorgeous platyhelminth worms, plus biological information.
Sea Slugs The Slug Site has great information on opisthobranch gastropods, plus a nudibranch of the week. Crinoids Charles Messing's Crinoid Page may lead to Victorian Era brain fever, bruxism, habitus fuscus (brown study), kicking of small inanimate objects, and hip dysplasia (if you're a German shepherd).
Horseshoe Crabs Horseshoe crabs have been around longer than dinosaurs, but these bluebloods are at the center of important vision and disease research. Stomatopods The Lurker's Guide to Stomatopods has a wealth of information on these fascinating crustaceans. The eyes have it!
NOAA NOAA's Coral Reefs and Associated Ecosystems is a coral reef data and information management system that integrates biological data from reef ecosystem monitoring and research programs with interrelated chemical, biological and physical data of surrounding marine areas. NOAA NOAA's Other Coral Reefs Site


Hellberg Lab The Hellberg Lab at Louisiana State University: Marine speciation and molecular evolution. The Neigel Lab at the University of Louisiana, Lafayette: Dispersal and genetic population structure in marine invertebrates, phylogeography, conservation biology.
Duffy Lab The Duffy Lab at the Virginia Institute of Marine Science: Ecology and evolution of marine animals and plants. Causes of speciation and maintenance of species diversity. Cunningham Lab The Cunningham Lab at Duke University: Molecular systematics and biogeography of marine organisms.

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