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202,464
Distance methods Invariant sites Insertion Deletion
, 2015
"... Twisted trees and inconsistency of tree estimation when gaps are treated as missing data – The impact of model misspecification in distance correctionsq ..."
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Twisted trees and inconsistency of tree estimation when gaps are treated as missing data – The impact of model misspecification in distance correctionsq
Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
, 2007
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Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution
 Systematic Biology
"... Abstract.—The models of nucleotide substitution used by most maximum likelihoodbased methods assume that the evolutionary process is stationary, reversible, and homogeneous. We present an extension of the Barry and Hartigan model, which can be used to estimate parameters by maximum likelihood (ML) ..."
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Cited by 11 (1 self)
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) when the data contain invariant sites and there are violations of the assumptions of stationarity, reversibility, and homogeneity. Unlike most ML methods for estimating invariant sites, we estimate the nucleotide composition of invariant sites separately from that of variable sites. We analyze a
General TimeReversible Distances with Unequal Rates across Sites: Mixing Γ and Inverse Gaussian Distributions with Invariant Sites
, 1997
"... This paper aims to explain to biologists the assumptions of these distances and to clarify some earlier misconceptions. Importantly, nearly all of the currently used distance estimates (including those of Tamura, 1992; Tamura and Nei, 1994) are special cases (restrictions) of the general timerevers ..."
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Cited by 49 (3 self)
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This paper aims to explain to biologists the assumptions of these distances and to clarify some earlier misconceptions. Importantly, nearly all of the currently used distance estimates (including those of Tamura, 1992; Tamura and Nei, 1994) are special cases (restrictions) of the general timereversible distance (see Zharkikh, 1994; Swofford et al., 1996)
Difficulties in Simulating the Internet
 IEEE/ACM Transactions on Networking
, 2001
"... Simulating how the global Internet behaves is an immensely challenging undertaking because of the network's great heterogeneity and rapid change. The heterogeneity ranges from the individual links that carry the network's traffic, to the protocols that interoperate over the links, to the & ..."
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Cited by 339 (8 self)
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, to the "mix" of different applications used at a site, to the levels of congestion seen on different links. We discuss two key strategies for developing meaningful simulations in the face of these difficulties: searching for invariants, and judiciously exploring the simulation parameter space. We
Critical percolation in the plane: conformal invariance, Cardy’s formula, scaling limits
 C. R. Acad. Sci. Paris Ser. I Math
, 2001
"... Abstract. We study scaling limits and conformal invariance of critical site percolation on triangular lattice. We show that some percolationrelated quantities are harmonic conformal invariants, and calculate their values in the scaling limit. As a particular case we obtain conformal invariance of t ..."
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Cited by 262 (9 self)
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Abstract. We study scaling limits and conformal invariance of critical site percolation on triangular lattice. We show that some percolationrelated quantities are harmonic conformal invariants, and calculate their values in the scaling limit. As a particular case we obtain conformal invariance
THE USE OF THE SONORAN DESERT AS A PSEUDOINVARIANT SITE FOR OPTICAL SENSOR CROSSCALIBRATION AND LONGTERM STABILITY MONITORING
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Maximum Likelihood Estimation of Phylogenetic Trees Is Consistent When Substitution Rates Vary According to the Invariable Sites plus Gamma Distribution. Systematic Biololgy
, 2001
"... workers have advocated the method of maximum likelihood (ML) for estimating phylogenetic trees from discrete character data, particularly nucleotide sequences, in part because it is thought to be consistent, i.e., it will converge on the true tree as more and more data are accumulated. In contrast, ..."
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Cited by 40 (0 self)
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workers have advocated the method of maximum likelihood (ML) for estimating phylogenetic trees from discrete character data, particularly nucleotide sequences, in part because it is thought to be consistent, i.e., it will converge on the true tree as more and more data are accumulated. In contrast, the method of maximum parsimony is known to converge, under certain conditions, on the wrong tree as more data are added (Felsenstein, 1978). Felsenstein's (1973) argument for the consistency of the ML method was based on earlier work (Wald, 1949) that demonstrated that maximum likelihood estimation of statistical parameters, such as means, variances, etc., is consistent under a wide variety of conditions. This work also guarantees the consistency of the ML estimate of the branch lengths of a phylogenetic tree, given the correct tree topology and nucleotide substitution model. However, as pointed out by several workers (e.g., Nei, 1987:325; Sai
The group Lasso for logistic regression
 Journal of the Royal Statistical Society, Series B
, 2008
"... Summary. The group lasso is an extension of the lasso to do variable selection on (predefined) groups of variables in linear regression models. The estimates have the attractive property of being invariant under groupwise orthogonal reparameterizations. We extend the group lasso to logistic regressi ..."
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Cited by 272 (11 self)
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Summary. The group lasso is an extension of the lasso to do variable selection on (predefined) groups of variables in linear regression models. The estimates have the attractive property of being invariant under groupwise orthogonal reparameterizations. We extend the group lasso to logistic
AmongSite Rate Variation and Its Impact on Phylogenetic Analyses
, 1996
"... ld follow a Poisson distribution. Fitch and Margoliasht counted the minimum number of nucleotide changes at each site in cytochrome c, and found that the Poisson distribution did not fit the data unless a certain num ber of 'invariant' and 'hypermutable' sites were excluded. The ..."
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Cited by 221 (11 self)
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ld follow a Poisson distribution. Fitch and Margoliasht counted the minimum number of nucleotide changes at each site in cytochrome c, and found that the Poisson distribution did not fit the data unless a certain num ber of 'invariant' and 'hypermutable' sites were excluded
Results 1  10
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202,464