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2013. AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite. Dictionary of Bioinformatics.
2004. BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView. Dictionary of Bioinformatics. :39-40,123-124,146,288-289,305,318,337,352,388,392,398-399,455,457,502,522,568.
2006. Conservation Patterns in cis-Elements Reveal Compensatory Mutations. Comparative GenomicsComparative Genomics. 4205
2006. Detection, Isolation, and Identification of Vibrio cholerae from the Environment. Current Protocols in MicrobiologyCurrent Protocols in Microbiology.
2010. Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
2008. Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology.
2004. Free-Living to Freewheeling: The Evolution of Vibrio cholerae from Innocence to Infamy. Infectious Disease and Host-Pathogen EvolutionInfectious Disease and Host-Pathogen Evolution.
2002. Fulfilling the promise of marine biotechnology. Marine biotechnology in the twenty-first century: problems, promise, and productsMarine biotechnology in the twenty-first century: problems, promise, and products.
2009. The Genus Vibrio and Related Genera. Practical handbook of microbiologyPractical handbook of microbiology.
2010. Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets. Bioinformatics Research and ApplicationsBioinformatics Research and Applications. 6053
1996. Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
2008. The Lattice Project: a Grid research and production environment combining multiple Grid computing models. Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities.
2008. The marine environment and human health: the cholera model. Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence.
1999. Multiple mechanisms of immune evasion by African trypanosomes. The Trypanosome Surface . :71-91.
2009. Salient Frame Detection for Molecular Dynamics Simulations. Scientific VisualizationScientific Visualization.
1997. Sequencing and mapping the African trypanosome genome. Trypanosomiasis and Leishmaniasis: Biology and Control . :51-63.
2004. A Tangled Bank: Reflections on the Tree of Life and Human Health. Assembling the Tree of LifeAssembling the Tree of Life.
1995. Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000