Literature

Authors	Year	Title
M. Haase	Submitted	Rapid and convergent evolution of parental care in hydrobiid gastropods from New Zealand
K. C. Nixon	Submitted	WinClada ver. 1.0000
A. B. Smith, Patterson C.	Submitted	The influence of taxonomic method on the perception of patterns of evolution
J. B. Losos, Ricklefs R. E.	2009	Adaptation and diversification on islands
J. Schultz, Wolf M.	2009	ITS2 sequence–structure analysis in phylogenetics: a how-to manual for molecular systematics
F. Bokma	2008	Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny
F. Bokma	2008	Bayesian estimation of speciation and extinction probabilities from (in)complete phylogenies
M. P. Cummings, Neel, M. C., Shaw, K. L.	2008	A genealogical approach to quantifying lineage divergence
H. M. Hines	2008	Historical biogeography, divergence times, and diversification patterns of bumble bees (Hymenoptera: Apidae: Bombus)
F. Legendre, Whiting, M. F., Bordereau, C., Cancello, Eliana, M., Evans, T. A., Grandcolas, P.	2008	The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors
A. Löytynoja, Goldman N.	2008	Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
L. Ricardo L. Simone, Wilkinson S.	2008	Comparative morphological study of some Tellinidae from Thailand (Bivalvia: Tellinoidea)
T. C. Stayton	2008	Is convergence surprising? An examination of the frequency of convergence in simulated datasets
Q. D. Atkinson, Meade, A., Venditti, C., Greenhill, S. J., Pagel, M.	2007	Languages evolve in punctuational bursts
D. Janies, Hill, A. W., Guralnick, R., Habib, F., Waltari, E., Wheeler, W. C.	2007	Genomic analysis and geographic visualization of the spread of avian influenza (H5N1)
M. A. Larkin, Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G.	2007	Clustal W and Clustal X version 2.0
A. Ø. Mooers	2007	The diversity of biodiversity
A. Stamatakis, Blagojevic, F., Nikolopoulos, D. S., Antonopoulos, C. D.	2007	Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell
R. Powell	2007	Is convergence more than an analogy? Homoplasy and its implications for macroevolutionary predictability
H. Quesada, Posada, D., Caballero, A., Morán, P., Rolán-Alvarez, E.	2007	Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail
K. D. Angielczyk, Fox D. L.	2006	Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record
D. A. Morrison	2006	Multiple sequence alignment for phylogenetic purposes
A. Stamatakis	2006	RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
W. C. Wheeler	2006	Dynamic homology and the likelihood criterion
W. C. Wheeler, Aagesen, L., Arango, C. P., Faivovich, J., Grant, T., D'Haese, C., Janies, D., Smith, W. L., Varón, A., Giribet, G.	2006	Dynamic homology and phylogenetic systematics: a unified approach using POY
W. C. Wheeler, Ramírez, M. J., Aagesen, L., Schulmeister, S.	2006	Partition-free congruence analysis: implications for sensitivity analysis
Z. Yang	2006	Computational molecular evolution
L. Aagesen	2005	Direct optimization, affine gap costs, and node stability
L. C. Anderson, Roopnarine P. D.	2005	Role of constraint and selection in the morphologic evolution of Caryocorbula (Mollusca: Corbulidae) from the Caribbean Neogene
Q. D. Atkinson, Gray R. D.	2005	Curious parallels and curious connections: phylogenetic thinking in biology and historical linguistics
K. M. A. Chan, Moore B. R.	2005	SymmeTREE: whole-tree analysis of differential diversification rates
B. Dayrat	2005	Ancestor-descendant relationships and the reconstruction of the Tree of Life
J. De Laet	2005	Parsimony and the problem of inapplicables in sequence data
J. Faivovich, Haddad, C. F. B., Garcia, P. C. A., Frost, D. R., Campbell, J. A.	2005	Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision
G. Giribet	2005	Generating implied alignments under direct optimization using POY
T. Grant, Kluge A. G.	2005	Stability, sensitivity, science and heurism
C. P. Meyer, Geller, J. B., Paulay, G.	2005	Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods
M. Spencer, Susko, E., Roger, A. J.	2005	Likelihood, parsimony, and heterogeneous evolution
A. Stamatakis, Ludwig, T., Meier, H.	2005	BRAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
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
F. E. Anderson, Swofford D. L.	2004	Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
O. R. P. Bininda-Emonds	2004	The evolution of supertrees
C. A. Brochu, Sumrall, C. D., Theodor, J. M.	2004	When clocks (and communities) collide: estimating divergence from molecules and the fossil record
K. de Queiroz	2004	The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference
T. A. Grantham	2004	The role of fossils in phylogeny reconstruction: why is it so difficult to integrate paleobiological and neontological evolutionary biology?
D. Graur, Martin W.	2004	Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision
B. Kolaczkowski, Thornton J. W.	2004	Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
G. Lecointre, Deleporte P.	2004	Total evidence requires exclusion of phylogenetically misleading data
L. P. Maia, Colato, A., Fontanari, J. !eF.	2004	Effect of selection on the topology of genealogical trees
J. G. Maisey, Naylor, G. J. P., Ward, David, J.	2004	Mesozoic elasmobranchs, neoselchian phylogeny and the rise of modern elasmobranch diversity

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