Spencer Muse's Research Page
(Please note: PowerMarker is no longer maintained or supported, but we continue to make it available for download for those who might find it useful in its final form)
CV
Publications
Greg Gibson and I recently published
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My research interests are in the areas of DNA sequence analysis and molecular evolution. I split my time roughly evenly between three broad areas: developing new statistical methodology, analyzing data through collaborations, and software devleopment.
My theoretical work is mainly in the area of molecular evolution. I am interested in developing new models of sequence evolution that are appropriate for protein-coding DNA sequences, and producing statistical procedures based on those tests.
My data analysis work spans several areas, but is again focused on molecular evolution. I have a long-running interest in the molecular evolution of plant genes. Laura Katz and I have recently been analyzing the evolution of protein-coding sequences in ciliates.
In recent years, my lab has moved heavily into software development. HyPhy is the result of a collaboration between myself and Sergei Kosakovsky Pond. HyPhy includes an interpreted batch language for scripting molecular evolutionary analyses, and an interface to allow you to carry out most analyses without bothering to learn the batch language. The main HyPhy page is at www.hyphy.org.
As part of his dissertation work, Jack Liu developed the PowerMarker package for managing and analyzing genetic marker data. PowerMarker has a powerful data manager coupled to an extensive set of marker analysis tools. PowerMarker is especially good for analyses of disequilibrium and population structure. Unfortunately, for career reasons Jack is no longer able to support PowerMarker, but it remains available for download at http://statgen.ncsu.edu/powermarker/