Literature

Authors	Year	Title
D. Posada, Crandall K. A.	1998	MODELTEST: testing the model of DNA substitution
R. Powell	2007	Is convergence more than an analogy? Homoplasy and its implications for macroevolutionary predictability
L. Prendini	2001	Species or supraspecific taxa as terminals in cladistic analysis? Groundplans versus exemplars revisited
R. D. Purchon, Brown D.	1969	Phylogenetic interrelationships among families of bivalve molluscs
A. Purvis, Katzourakis, A., Agapow, P. - M.	2002	Evaluating phylogenetic tree shape: ywo modifications to Fusco & Cronk's method
K. de Queiroz	2004	The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference
A. de Queiroz, Donoghue, M. J., Kim, junhyong	1995	Separate versus combined analysis of phylogenetic evidence
H. Quesada, Posada, D., Caballero, A., Morán, P., Rolán-Alvarez, E.	2007	Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail
W. - E. Reif	2004	Problematic issues of cladistics: 3. Homology and apomorphy; ontology versus operationalism
W. - E. Reif	2003	Problematic issues of cladistics: 1. Ancestor recognition and phylogenetic classification
F. Rodriguez, Oliver, , J. F., Marin, A., Medina, J. R.	1990	The general stochastic model of nucleotide substitutions
A. Rokas, Williams, B. L., King, N., Carroll, S. B.	2003	Genome-scale approaches to resolving incongruence in molecular phylogenies
A. Rzhetsky, Nei M.	1992	A simple method for estimating and testing minimum-evolution trees
A. Rzhetsky, Nei M.	1992	Statistical properties of the ordinary least-squares, generalized least-squares, and minimum evolution methods of phylogenetic inference
N. Saitou	1989	A theoretical study of the underestimation of brench length by the maximum parsimony principle
M. Sanderson, Donoghue M. J.	1996	Reconstructing shifts in diversification rates on phylogenetic trees
D. Schluter, Price, T., Mooers, A. Ø., Ludwig, D.	1997	Likelihood of ancestor atates in adaptive radiation
S. Schulmeister, Wheeler, W. C., Carpenter, J. M.	2002	Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
J. Schultz, Wolf M.	2009	ITS2 sequence–structure analysis in phylogenetics: a how-to manual for molecular systematics
T. R. Schultz, Engel, M. S., Ascher, J. S.	2001	Evidence for the origin of eusociality in the corbiculate bees (Hymenoptera: Apidae)
B. Schwikowski, Vingron M.	1997	The deferred path heuristic for the generalized tree alignment problem
A. Seilacher	1991	Self-organizing mechanisms in morphogenesis and evolution
M. E. Siddall	1998	Stratigraphic fit to phylogenies: a proposed solution
L. Ricardo L. Simone, Wilkinson S.	2008	Comparative morphological study of some Tellinidae from Thailand (Bivalvia: Tellinoidea)
Z. Skála, Zrzavπ J.	1994	Phylogenetic reticulations and cladistics: discussion of methodological concepts
A. B. Smith	1998	What does palaeontology contribute to systematics in a molecular world?
A. B. Smith	1994	Systematics and the fossil record: documenting evolutionary patterns
A. B. Smith	1994	Rooting molecular trees: problems and strategies
A. B. Smith, Littlewood D. T. J.	1994	Paleontological data and molecular phylogenetic analysis
A. B. Smith, Patterson C.	Submitted	The influence of taxonomic method on the perception of patterns of evolution
A. B. Smith, Peterson K. J.	2002	Dating the time of origin of major clades: molecular clocks and the fossil record
W. L. Smith, Wheeler W. C.	2004	Polyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data
E. Sober	1983	Parsimony in systematics: philosophical issues
M. Spencer, Susko, E., Roger, A. J.	2005	Likelihood, parsimony, and heterogeneous evolution
A. Stamatakis	2006	RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
A. Stamatakis, Blagojevic, F., Nikolopoulos, D. S., Antonopoulos, C. D.	2007	Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell
A. Stamatakis, Ludwig, T., Meier, H.	2005	BRAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
T. C. Stayton	2008	Is convergence surprising? An examination of the frequency of convergence in simulated datasets
C. A. Stepien, Hubers, A. N., Skidmore, J. L.	1999	Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA
E. E. Strong, Lipscomb D.	1999	Character coding and inapplicable data
D. L. Sullivan	1996	Combining data with different distributions of among-site variation
J. Sullivan, Abdo, Z., Joyce, P., Swofford, D. L.	2005	Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation
J. Sullivan, Holsinger, K. E., Simon, C.	1996	The effect of topology on estimates of among-site rate variation
D. L. Swofford	1991	When are phylogeny estimates from molecular and morphological data incongruent?
D. L. Swofford, Waddell, P. J., Huelsenbeck, J. P., Foster, P. G., Lewis, P. O., Rogers, J. S.	2001	Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
K. Tamura, Nei M.	1993	Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
S. Tavaré	1986	Some probabilistic and statistical problems in the analysis of DNA sequences
A. R. Templeton	2001	Using phylogeographic analyses of gene trees to test species status and processes
A. R. Templeton	1998	Nested clade analysis of phylogenetic data: testing hypotheses about gene flow and population history
A. R. Templeton	1983	Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes

Authors