Evolutionary trees from DNA sequences: A maximum likelihood approach

By Joseph Felsenstein. Journal of Molecular Evolution, 2005

12,324 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e0cbb949d062a1134c4d98924f51312090e76514

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Citations in the corpus

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics (2011, methodology): “We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference.”
Bayesian Phylogeography Finds Its Roots (2009, methodology): “CTMCs are the same processes one commonly exploits to model sequence character evolution [15,50].”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, methodology): “INDELible also includes the general time-reversible model (GTR or REV, Tavaré 1984; Yang 1994a) and many commonly used models that are its special cases, such as JC69 (Jukes and Cantor 1969), K80 (Kimura 1980), K81 (Kimura 1981), F81 (Felsenstein 1981), F84 (Felsenstein, DNAML program since 1984, PH”
Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci (2003, methodology): “terion (Felsenstein 1981) as implemented in POY using direct optimization for the combined molecular data set.”
Efficient approximations for learning phylogenetic HMM models from data (2004, methodology): “maximum likelihood, Bayesian information criterion) and some heuristic search method is used to find a tree or set of trees with high scores (e.g. Felsenstein, 1981; Durbin et al., 1998).”
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. (2003, methodology): “For example, the assumptions that each nucleotide or amino acid substitutes for the other at the same average rate, and that this average rate is constant across sites (Neyman 1971; Felsenstein 1981), have both given way to more realistic alternatives (Whelan, Liò, and Goldman 2001).”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, methodology): “We note that f[XjT , θ] is the likelihood of the tree and sequence model parameters, which we calculate with Felsenstein’s pruning algorithm (71, 72); f[T jλ, μ, ψ, ρ, x1] is the prior probability of the unresolved FBD tree given in Eq.”
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. (2011, methodology): “MEGA5 now provides the ML method to infer evolutionary trees and conduct the bootstrap test for nucleotide and amino acid alignments (Felsenstein 1981, 1985).”
Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes (2012, methodology): “The most appropriate models of molecular evolution for maximum likelihood (ML; Felsenstein, 1981) and Bayesian (Rannala & Yang, 1996; Yang & Rannala, 1997) phylogenetic analyses were selected using a Bayesian information criterion, as implemented in DT_ModSel (Minin et al.”
Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, background): “Hydrocallis, the GTRþG model for the trnL intron and the trnL-trnF spacer, and the F81 model (Felsenstein 1981) for the P8 character set of subgg.”
Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. (2013, methodology): “The actual calculation of the likelihood over the whole tree utilizes the “pruning algorithm” (Felsenstein 1973, 1981) to sum over the inner node values that we cannot observe: With error in the measurements, a naı¨ve inference based on use of the W ’s instead of the X ’s leads to: P ð W n j l , …”
PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. (2013, background): “In particular, it is a mixture of F81 (Felsenstein 1981) processes, such that, upon a substitution, the probability of the final state does not depend on the initial state.”
Characterising invasion processes with genetic data: an Atlantic clade of Clavelina lepadiformis (Ascidiacea) introduced into Mediterranean harbours (2003, methodology): “A haplotype tree was then estimated under the maximum likelihood criterion (ML; Felsenstein, 1981), with the parameter estimates obtained under the best-fit model.”
Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times (2006, methodology): “Method 4: Character-based maximum likelihood clock optimization (Felsenstein, 1981; Swofford et al ., 1996)”
Multiple fossil calibrations, nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae, Pinnipedia) (2010, methodology): “A likelihood ratio test for clock-like evolution (Felsenstein, 1981) was performed using paup* v.”