Literature

AuthorsYearTitlesort descending
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
T. Jiang, Lawler, E. L., Wang, A.1994Aligning sequences via an evolutionary tree: complexity and approximation
O. Gotoh1982An improved algorithm for matching biological sequences
X. Xia, Xie, Z., Salemi, M., Chen, L., Wang, Y.2003An index of substitution saturation and its application
M. Björklund1999Are third positions really that bad? A test using vertebrate cytochrome b
A. Stamatakis, Ludwig, T., Meier, H.2005BRAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
J. Felsenstein1978Cases in which parsimony or compatibility methods will be positively misleading
D. L. Sullivan1996Combining data with different distributions of among-site variation
M. W. Allard, Farris, J. S., Carpenter, J. M.1999Congruence among mammalian mitochondrial genes
A. R. Templeton1983Convergent evolution and nonparametric inferences from restriction data and DNA sequences
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
F. Bokma2002Detection of punctuated equilibrium from molecular phylogenies
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
G. C. Conant, Lewis P. O.2001Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference
K. Tamura, Nei M.1993Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
A. Stamatakis, Blagojevic, F., Nikolopoulos, D. S., Antonopoulos, C. D.2007Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell
D. Graur, Li W. - H.2000Fundamentals of molecular evolution
M. Källersjö, Albert, V. A., Farris, J. S.1999Homoplasy increases phylogenetic structure
D. M. Hillis1996Inferring complex phylogenies
N. Galtier, Gouy M.1995Inferring phylogenies from DNA sequences of unequal base compositions
M. Pagel1999Inferring the historical patterns of biological evolution
J. Schultz, Wolf M.2009ITS2 sequence–structure analysis in phylogenetics: a how-to manual for molecular systematics
D. Posada, Buckley T. R.2004Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests
M. Nei, Kumar S.2000Molecular evolution and phylogenetics
R. D. M. Page, Holmes E. C.1998Molecular evolution: a phylogenetic approach
Z. Yang1998On the best evolutionary rate for phylogenetic analysis
W. C. Wheeler, Ramírez, M. J., Aagesen, L., Schulmeister, S.2006Partition-free congruence analysis: implications for sensitivity analysis
J. Felsenstein1985Phylogenies and the comparative method
A. Stamatakis2006RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
P. J. Lockhart, Steel, M. A., Hendy, M. D., Penny, D.1994Recovering evolutionary trees under a more realistic model of sequence evolution
D. P. Mindell, Honeycutt R. L.1990Ribosomal RNA in vertebrates: evolution and phylogenetic applications
F. E. Anderson, Swofford D. L.2004Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
A. Knight, Mindell D. P.1993Substitution bias weighting of DNA sequence evolution and the phylogenetic position of Fea's viper
F. Bokma2003Testing for equal rates of cladogenesis in diverse taxa
B. Schwikowski, Vingron M.1997The deferred path heuristic for the generalized tree alignment problem
J. Sullivan, Holsinger, K. E., Simon, C.1996The effect of topology on estimates of among-site rate variation
R. Holmquist1983Transitions and transversions in evolutionary descent: an approach to understanding
A. R. Templeton2001Using phylogeographic analyses of gene trees to test species status and processes
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith