Peter J Waddell

Summary

Affiliation: University of South Carolina
Country: USA

Publications

  1. ncbi request reprint Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
    Peter J Waddell
    Department of Statistics, University of South Carolina, Columbia 29208, USA
    Mol Phylogenet Evol 28:197-224. 2003
  2. ncbi request reprint Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data
    Peter J Waddell
    Department of Statistics and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Genome Inform 13:82-92. 2002
  3. ncbi request reprint Measuring the fit of sequence data to phylogenetic model: allowing for missing data
    Peter J Waddell
    Department of Statistics, Department of Biological Sciences, University of South Carolina, Columbia, USA
    Mol Biol Evol 22:395-401. 2005
  4. doi request reprint Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests
    Peter J Waddell
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
    J Mol Evol 69:289-99. 2009
  5. ncbi request reprint Phylogenetic methodology for detecting protein interactions
    Peter J Waddell
    Department of Statistics and Department of Biological Sciences, University of South Carolina, Columbia, SC 29203, USA
    Mol Biol Evol 24:650-9. 2007
  6. ncbi request reprint TALI: local alignment of protein structures using backbone torsion angles
    Xijiang Miao
    Department of Computer Science and Engineering, University of South Carolina, 301 Main Street, Columbia, SC 29208, USA
    J Bioinform Comput Biol 6:163-81. 2008
  7. pmc Structure of Penaeus stylirostris densovirus, a shrimp pathogen
    Bärbel Kaufmann
    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907 2054, USA
    J Virol 84:11289-96. 2010
  8. ncbi request reprint Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires
    Yu Hsin Lin
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Gene 294:119-29. 2002
  9. doi request reprint LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences
    Paul D Waters
    Research School of Biological Sciences, The Australian National University, Canberra, Australia
    Methods Mol Biol 422:227-37. 2008
  10. ncbi request reprint Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome
    Joshua S Rest
    Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109 1079, USA
    Mol Phylogenet Evol 29:289-97. 2003

Collaborators

Detail Information

Publications10

  1. ncbi request reprint Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
    Peter J Waddell
    Department of Statistics, University of South Carolina, Columbia 29208, USA
    Mol Phylogenet Evol 28:197-224. 2003
    ..g., rare indels, gene rearrangement, and SINE data)...
  2. ncbi request reprint Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data
    Peter J Waddell
    Department of Statistics and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Genome Inform 13:82-92. 2002
    ..Since many of the methods studied are very fast computationally, there is no reason to ignore stochastic error even with the slowest ML or likelihood based methods...
  3. ncbi request reprint Measuring the fit of sequence data to phylogenetic model: allowing for missing data
    Peter J Waddell
    Department of Statistics, Department of Biological Sciences, University of South Carolina, Columbia, USA
    Mol Biol Evol 22:395-401. 2005
    ..The methods are also useful with Hadamard conjugations (spectral analysis) and are illustrated with these and with ML evolutionary models that allow site-rate variability...
  4. doi request reprint Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests
    Peter J Waddell
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
    J Mol Evol 69:289-99. 2009
    ..g., bootstrap) report...
  5. ncbi request reprint Phylogenetic methodology for detecting protein interactions
    Peter J Waddell
    Department of Statistics and Department of Biological Sciences, University of South Carolina, Columbia, SC 29203, USA
    Mol Biol Evol 24:650-9. 2007
    ..Use of edge-length vectors is compared and contrasted with correlated distance methods, correlated rates methods, and site-specific evidence of coevolution...
  6. ncbi request reprint TALI: local alignment of protein structures using backbone torsion angles
    Xijiang Miao
    Department of Computer Science and Engineering, University of South Carolina, 301 Main Street, Columbia, SC 29208, USA
    J Bioinform Comput Biol 6:163-81. 2008
    ..Availability: http://redcat.cse.sc.edu/index.php/Project:TALI/...
  7. pmc Structure of Penaeus stylirostris densovirus, a shrimp pathogen
    Bärbel Kaufmann
    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907 2054, USA
    J Virol 84:11289-96. 2010
    ..However, most of the surface loops have little structural resemblance to any of the known parvoviral capsid proteins...
  8. ncbi request reprint Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires
    Yu Hsin Lin
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Gene 294:119-29. 2002
    ..Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms...
  9. doi request reprint LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences
    Paul D Waters
    Research School of Biological Sciences, The Australian National University, Canberra, Australia
    Methods Mol Biol 422:227-37. 2008
    ....
  10. ncbi request reprint Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome
    Joshua S Rest
    Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109 1079, USA
    Mol Phylogenet Evol 29:289-97. 2003
    ..We also report a unique configuration for the mitochondrial genome of Sphenodon, including two tRNA(Lys) copies and an absence of ND5, tRNA(His), and tRNA(Thr) genes...