Literature

AuthorsYearsort descendingTitle
J. Felsenstein1978Cases in which parsimony or compatibility methods will be positively misleading
O. Gotoh1982An improved algorithm for matching biological sequences
R. Holmquist1983Transitions and transversions in evolutionary descent: an approach to understanding
A. R. Templeton1983Convergent evolution and nonparametric inferences from restriction data and DNA sequences
J. Felsenstein1985Phylogenies and the comparative method
N. Saitou, Nei M.1987The neighbor-joining method: a new method for reconstructing phylogenetic trees
J. Hein1989A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given
J. Hein1989A tree reconstruction method that is economical in the number of pairwise comparisons used
D. P. Mindell, Honeycutt R. L.1990Ribosomal RNA in vertebrates: evolution and phylogenetic applications
A. Knight, Mindell D. P.1993Substitution bias weighting of DNA sequence evolution and the phylogenetic position of Fea's viper
K. Tamura, Nei M.1993Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
T. Jiang, Lawler, E. L., Wang, A.1994Aligning sequences via an evolutionary tree: complexity and approximation
P. J. Lockhart, Steel, M. A., Hendy, M. D., Penny, D.1994Recovering evolutionary trees under a more realistic model of sequence evolution
N. Galtier, Gouy M.1995Inferring phylogenies from DNA sequences of unequal base compositions
G. Giribet, Carranza, S., Baguna, J., Riutort, M., Ribera, C.1996First molecular evidence for the existence of a Tardigrada + Arthropoda clade
D. M. Hillis1996Inferring complex phylogenies
D. L. Sullivan1996Combining data with different distributions of among-site variation
J. Sullivan, Holsinger, K. E., Simon, C.1996The effect of topology on estimates of among-site rate variation
L. S. Adamkewicz, Harasewych, M. G., Blake, J., Saudek, D., Bult, C. J.1997A molecular phylogeny of the bivalve mollusks
B. Schwikowski, Vingron M.1997The deferred path heuristic for the generalized tree alignment problem
S. L. Messenger, McGuire J. A.1998Morphology, molecules, and the phylogenetics of cetaceans
R. D. M. Page, Holmes E. C.1998Molecular evolution: a phylogenetic approach
Z. Yang1998On the best evolutionary rate for phylogenetic analysis
M. W. Allard, Farris, J. S., Carpenter, J. M.1999Congruence among mammalian mitochondrial genes
M. Björklund1999Are third positions really that bad? A test using vertebrate cytochrome b
M. Källersjö, Albert, V. A., Farris, J. S.1999Homoplasy increases phylogenetic structure
M. Pagel1999Inferring the historical patterns of biological evolution
Z. Yang, Yoder A. D.1999Estimation of the transition/transversion rate bias and species sampling
D. Graur, Li W. - H.2000Fundamentals of molecular evolution
M. Nei, Kumar S.2000Molecular evolution and phylogenetics
Steiner, G., Hammer S.2000Molecular phylogeny of the Bivalvia inferred from 18S rDNA sequences with particular reference to the Pteriomorphia
G. C. Conant, Lewis P. O.2001Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference
W. R. Hoeh, Bogan, A. E., Heard, W. H.2001A phylogenetic perspective on the evolution of morphological and reproductive characteristics in the Unionoida
A. R. Templeton2001Using phylogeographic analyses of gene trees to test species status and processes
W. C. Wheeler2001Homology and DNA sequence data
F. Bokma2002Detection of punctuated equilibrium from molecular phylogenies
F. Bokma2003Testing for equal rates of cladogenesis in diverse taxa
X. Xia, Xie, Z., Salemi, M., Chen, L., Wang, Y.2003An index of substitution saturation and its application
F. E. Anderson, Swofford D. L.2004Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
D. Posada, Buckley T. R.2004Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests
A. Stamatakis, Ludwig, T., Meier, H.2005BRAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
D. L. Graf, Cummings K. S.2006Palaeoheterodont diversity (Mollusca: Trigonioida+Unionoida): what we know and what we wish we knew about freshwater mussel evolution
P. M. Mikkelsen, Bieler, R., Kappner, I., Rawlings, T. A.2006Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules
A. Stamatakis2006RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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. Wheeler, Ramírez, M. J., Aagesen, L., Schulmeister, S.2006Partition-free congruence analysis: implications for sensitivity analysis
A. Stamatakis, Blagojevic, F., Nikolopoulos, D. S., Antonopoulos, C. D.2007Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell
F. Bokma2008Detection 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
D. Takakura, Wada, K. T., Kobayashi, T., Masaoka, T., Samata, T.2008Phylogenetic relationships of several pearl oyster species in Pinctada (Pteriidae ; Bivalvia) inferred from mitochondrial 12S rDNA and cytochrome c oxidase subunit I genes sequences
W. Renema, Bellwood, D. R., Braga, J. C., Bromfield, K., Hall, R., Johnson, K. G., Lunt, P., Meyer, C. P., McMonagle, L. B., Morley, R. J., O’Dea, A., Todd, J. A., Wesselingh, F. P., Wilson, M. E. J., Pandolfi, J. M.2008Hopping hotspots: global shifts in marine biodiversity

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