A space-time process model for the evolution of DNA sequences.

By Ziheng Yang. 1995

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Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, neutral): “The ‘LG’ model was applied with 12 substitution rate categories 67,68 and the tree topology, branch lengths and the substitution model parameters were optimized.”
Bayesian Phylogeography Finds Its Roots (2009, methodology): “To model sequence evolution, we employ the [29] (HKY85) CTMC model of nucleotide substitution; we include discrete gamma-distributed rate variation [30] and assume an unknown, constant population-size coalescent process prior over the unknown phylogeny [31].”
Efficient approximations for learning phylogenetic HMM models from data (2004, background): “There have been numerous efforts to relax these assumptions (e.g. Siepel and Haussler, 2003; Yang, 1995; Felsenstein and Churchill, 1996; Strimmer and Moulton, 2000; Nakhleh et al ., 2003).”
A Simple and Robust Statistical Test for Detecting the Presence of Recombination (2006, methodology): “To achieve this, two random variables Yi and Yi11 were drawn from a bivariate normal distribution with correlation rN and transformed into two marginally distributed gamma random variables Zi and Zi11 with correlation rG (Yang 1995).”
Phylogenetic Analysis by Maximum Likelihood (PAML) (2002, methodology): “…value for alpha , and ncatG is then the number of categories for the discrete-gamma model ( baseml ). fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where ρ (rho) is the correlation parameter of the auto-discrete-gamma model (Yang 1995).”
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. (2007, methodology): “…program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Yang 1995; Felsenstein and Churchill 1996; Siepel and Haussler 2005).”
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. (2004, methodology): “For example, the standard bootstrap method in which individual sites are sampled is inappropriate for models that incorporate correlation in rates (Yang, 1995; Felsenstein and Churchill, 1996) because the sampling procedure destroys the autocorrelation structure of rates in the bootstrap matrices.”
PhyLAT: a phylogenetic local alignment tool (2012, background): “Classical results from phylogeny (Yang, 1995) give the theory needed to construct a maximum-likelihood alignment between a query sequence and a reference multiple alignment, provided that neither query nor reference contains gaps.”
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis (2003, methodology): “This strategy is not guaranteed to find the true maximum-likelihood estimate of ( , α, λ), but it seems to provide a close approximation, because the other parameters are insensitive to λ (as noted by Yang [43]).”
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. (2004, result): “…our analysis is robust with respect to the phylogeny, a fact which is not surprising, as similar conclusions have been reached by authors studying the sensitivity of rate across site parameters (Yang 1995), or of tests of model comparison (Posada and Crandall 2001), to the underlying phylogeny.”