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A structural EM algorithm for phylogenetic inference (2002)

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by Matan Ninio , B. Sc , Dr. Nir Friedman , Danny Dolev , Matan Ninio
Venue:Journal of Computational Biology
Citations:40 - 7 self
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BibTeX

@ARTICLE{Ninio02astructural,
    author = {Matan Ninio and B. Sc and Dr. Nir Friedman and Danny Dolev and Matan Ninio},
    title = {A structural EM algorithm for phylogenetic inference},
    journal = {Journal of Computational Biology},
    year = {2002},
    volume = {9},
    pages = {331--353}
}

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Abstract

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Citations

6236 Maximum likelihood from incomplete data via EM algorithm - Dempster, Laird, et al. - 1977
2802 Optimization by Simulated Annealing - Kirkpatrick, Gelati, et al. - 1983
1042 Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol - Saitou - 1987
541 Evolutionary Trees from DNA sequences: a maximum likelihood approach - Felsenstein - 1981
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487 Approximating discrete probability distributions with dependence trees - Chow, Liu - 1968
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229 Evolution of protein molecules - Jukes, Cantor - 1969
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186 Inferring Phylogenies Sinauer Associates - Felsenstein - 2004
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128 Yang Z: A codon-based model of nucleotide substitution for protein-coding DNA sequences - Goldman - 1994
107 Learning belief networks in the presence of missing values and hidden variables - Friedman - 1997
93 Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 1988, 22:521-565. Page 16 of 16 (page number not for citation purposes - Felsenstein
89 fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood - Olsen, Matsuda, et al. - 1994
88 Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites - Yang - 1993
80 How to get a perfectly random sample from a generic Markov chain and generate a random spanning tree of a directed graph - Propp, Wilson - 1998
65 Disk-covering, a fast-converging method for phylogenetic tree reconstruction - Huson, Nettles, et al. - 1999
56 A measure of asymptotic eciency for test of a hypothesis based on the sum of observations - Cherno - 1952
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31 A Genetic Algorithm for Maximum Likelihood Phylogeny Inference Using Nucleotide Sequence Data. Mol Biol Evol - Lewis - 1998
29 Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time - Graham, Foulds - 1982
26 A simple model for estimating evolutionary rates of base substitiutions through comparative studies of nucleotide sequences - Kimura - 1980
21 Gascuel O: Quartet-Based Phylogenetic Inference: Improvements and - Ranwez - 2001
18 Warnow T., “Solving large scale phylogenetic problems using DCM2”, in - Huson, Vawter - 1999
10 Where do rodents fit? Evidence from the complete mitochondrial genome of sciurus vulgaris - Reyes, Gissi, et al. - 2000
6 Discovering the structure of complex dynamic systems - Boyen, Friedman - 1999
4 LVB 1.0: Reconstructing Evolution with Parsimony and Simulated Annealing - Barker - 1997
4 Computationally di cult parsimony problems in phylogenetic systematics - Day - 1983
4 Parsimonious phylogenetic trees in metric spaces and simulated annealing - Dress, Kruger - 1987
3 Multiple local maxima for likelihoods of phylogenetic trees: a simulation study - Rogers, Swofford - 1999
1 Modeling of Molecular Evolution and Maximum Likelihood Inference of Molecular Phylogeny - Adachi - 1995
1 Weight perturbations for escaping local maxima in learning graphical models, Submitted for publication - Elidan, Ninio, et al. - 2001
1 Algorithmic improvements and biological applications of maximum likelihood methods of reconstruction of ancestral amino-acid sequences - Pupko - 2000
1 PAUP*beta: Phylogenetic analysis Using Parsimony - Swoord - 1998
1 CLUSTAL W: Improving the sensitivity of progressie multiple sequence alignment through sequence weighting, position specific gep penalties and weight matrix choice - Thompson, Higgins - 1994
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