Literature

Authorssort ascendingYearTitle
A. D. Yoder, Irwin, J. A., Payseur, B. A.2001Failure of the ILD to determine data combinability for slow Loris phylogeny
Z. Yang1993Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
Z. Yang1998On the best evolutionary rate for phylogenetic analysis
Z. Yang1994Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
Z. Yang1996Phylogenetic analysis using parsimony and likelihood methods
Z. Yang2006Computational molecular evolution
X. Xia, Xie, Z., Salemi, M., Chen, L., Wang, Y.2003An index of substitution saturation and its application
X. Xia, Xie Z.2001DAMBE: software package for data analysis in molecular biology and evolution
M. A. Wills2001Morphological disparity: a primer
M. A. Wills1999Congruence between phylogeny and stratigraphy: randomization tests and the gap excess ratio
W. C. Wheeler, Ramírez, M. J., Aagesen, L., Schulmeister, S.2006Partition-free congruence analysis: implications for sensitivity analysis
W. C. Wheeler, Aagesen, L., Arango, C. P., Faivovich, J., Grant, T., D'Haese, C., Janies, D., Smith, W. L., Varón, A., Giribet, G.2006Dynamic homology and phylogenetic systematics: a unified approach using POY
W. C. Wheeler1990Nucleic acid sequence phylogeny and random outgroups
W. C. Wheeler1995Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data
W. Wheeler1999Fixed character states and the optimization of molecular sequence data
W. C. Wheeler1999Measuring topological congruence by extending character techniques
W. Wheeler2001Homology and the optimization of DNA sequence data
W. C. Wheeler2003Iterative pass optimization of sequence data
W. C. Wheeler2003Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search
W. C. Wheeler2006Dynamic homology and the likelihood criterion
J. Wakeley1993Substitution-rate variation among sites and the estimation of transition bias
P. J. Wagner1998A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa
P. J. Wagner2000Exhaustion of morphologic character states among fossil taxa
M. G. P. Van Veller, Brooks D. R.2001When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography
J. D. Thompson, Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G.1997The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
A. R. Templeton1983Convergent evolution and nonparametric inferences from restriction data and DNA sequences
A. R. Templeton1983Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes
A. R. Templeton1998Nested clade analysis of phylogenetic data: testing hypotheses about gene flow and population history
A. R. Templeton2001Using phylogeographic analyses of gene trees to test species status and processes
S. Tavaré1986Some probabilistic and statistical problems in the analysis of DNA sequences
K. Tamura, Nei M.1993Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
D. L. Swofford, Waddell, P. J., Huelsenbeck, J. P., Foster, P. G., Lewis, P. O., Rogers, J. S.2001Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
D. L. Swofford1991When are phylogeny estimates from molecular and morphological data incongruent?
J. Sullivan, Holsinger, K. E., Simon, C.1996The effect of topology on estimates of among-site rate variation
J. Sullivan, Abdo, Z., Joyce, P., Swofford, D. L.2005Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation
D. L. Sullivan1996Combining data with different distributions of among-site variation
E. E. Strong, Lipscomb D.1999Character coding and inapplicable data
C. A. Stepien, Hubers, A. N., Skidmore, J. L.1999Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA
T. C. Stayton2008Is convergence surprising? An examination of the frequency of convergence in simulated datasets
A. Stamatakis, Ludwig, T., Meier, H.2005BRAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
A. Stamatakis, Blagojevic, F., Nikolopoulos, D. S., Antonopoulos, C. D.2007Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell
A. Stamatakis2006RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
M. Spencer, Susko, E., Roger, A. J.2005Likelihood, parsimony, and heterogeneous evolution
E. Sober1983Parsimony in systematics: philosophical issues
W. L. Smith, Wheeler W. C.2004Polyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data
A. B. Smith, Peterson K. J.2002Dating the time of origin of major clades: molecular clocks and the fossil record
A. B. Smith, Patterson C.SubmittedThe influence of taxonomic method on the perception of patterns of evolution
A. B. Smith, Littlewood D. T. J.1994Paleontological data and molecular phylogenetic analysis
A. B. Smith1994Systematics and the fossil record: documenting evolutionary patterns
A. B. Smith1994Rooting molecular trees: problems and strategies

Pages

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith