Evolution maximum likelihood

Other methods such as Genetic Algorithm based on evolution principles, maximum entropy method based on Bayesian theory, and maximum likelihood methods have also been developed. ... 

There seem to be three problems here. Maximum likelihood techniques are rarely applied to morphological data because (unlike molecular data) there is little empirical justification for assuming certain patterns or models of evolution. For instance, the arguments of bone fusion or fragmentation of the skull of crossopterygian fishes were basically sterile. Second, likelihood estimates of the fossil record only measure how well we have sampled the available... 

The Reconstruction of Evolution The Principle of Minimum Evolution The Influence of Traditional Procedures Maximum Likelihood Extremum Principles in Science Epilogue References... 

Kishino, H., Miyata, T., and Hasegawa, M. (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts./o r a/ of Molecular Evolution, 31,151-160. 

Kishino, H. and Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Homi-noide2i. Journal of Molecular Evolution, 29,170-179. 

Phylogenetic relationships within the Ptychomniales were evalnated using maximum likelihood and Bayesian inference of chloroplast and mitochondrial DNA sequence data. Maximum likelihood and maximum parsimony were employed to study evolution of 18 morphological characters within... 

Figure 7.1 Minimum evolution (ME) tree based on LogDet distances of nearly complete rRNA sequences (18S-28S-partial S.8S). Rate heterogeneity among sites was approximated by assuming the proportion of invariable sites, to be 0.615 (see text for justification). Numbers above branches represent bootstrap values the lower numbers represent the ME bootstrap values, the upper numbers represent parsimony bootstrap values, and the middle numbers represent maximum-likelihood (ML) bootstrap values. Note the strong ME and ML bootstrap support for the lamprey+hagfish (cyclostome) clade.

Strimmer, K. and von Haeseler, A. (1996) Quartet puzzling a quartet maximum-likelihood method for reconstructing tree topologies . Molecular Biology and Evolution, 13, 964-9. 

ABSTRACT This paper illustrates the main features of the MUlti-STAte DEgradation Process analysis Tool (MUSTADEPT), a new software tool which allows quantitatively describing the evolution of the degradation process of an industrial equipment, modeled as a discrete-state transport process. Two different, complementary approaches are offered. One is based on statistics, specifically the Maximum Likelihood Estimation (MLE) technique to estimate the parameters of the degradation process model and the Fisher Information Matrix for evaluating the uncertainty associated to the estimates. The other approach relies on information elicited from experts and describes and propagates the associated uncertainty within the DSTE framework. In both cases, the probabilities that the component occupies the different degradation states over time are estimated with the associated uncertainties. 

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