Peter J Waddell
Affiliation: University of South Carolina
- Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon modelsPeter 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)...
- Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence dataPeter 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...
- Measuring the fit of sequence data to phylogenetic model: allowing for missing dataPeter 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...
- Measuring fit of sequence data to phylogenetic model: gain of power using marginal testsPeter J Waddell
Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
J Mol Evol 69:289-99. 2009..g., bootstrap) report...
- Phylogenetic methodology for detecting protein interactionsPeter 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...
- TALI: local alignment of protein structures using backbone torsion anglesXijiang 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..The inference of the evolutionary tree of class II aminoacyl-tRNA synthetase shows the potential for TALI in estimating protein structural evolution and in identifying structural divergence among homologous structures...
- Structure of Penaeus stylirostris densovirus, a shrimp pathogenBärbel 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...
- Pika and vole mitochondrial genomes increase support for both rodent monophyly and gliresYu 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...
- LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequencesPaul D Waters
Research School of Biological Sciences, The Australian National University, Canberra, Australia
Methods Mol Biol 422:227-37. 2008....
- Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genomeJoshua 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...