Phyloclustering -- Phylogenetic Clustering

Phyloclustering -- Phylogenetic Clustering

Phyloclustering
Overview
Method
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Jargon

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Section: Jargon

Some terminologies used in phyclust will be listed in the following. The details can be found on wiki, google, or in literatures.

Phylogenetics

Instantaneous rate matrix $\boldsymbol{Q}$
- JC69
  Jukes, T. H. and Cantor, C. R. 1969. "Evolution of protein molecules." Mammalian Protein Metabolism. Academic Press. 3:21-132.
- K80
  Kimura, M. 1980. "A Simple Method for Estimating Evolutionary Rates of Base Substitutions Through Comparative Studies of Nucleotide Sequences." Journal of Molecular Evolution. 16:111--120.
- HKY85
  Hasegawa, M. and Kishino, H. and Yano, T. 1985. "Dating of the human-ape splitting by a molecular clock of mitochondrial DNA." Journal of Molecular Evolution. 22:160--174.
Identifier (EE, EV, VE, VV) for clusters

     Identifier $\boldsymbol{Q}$
     EE $\boldsymbol{Q}_1 = \boldsymbol{Q}_2 = \cdots = \boldsymbol{Q}_K$ $t_1 = t_2 = \cdots = t_K$
     EV $\boldsymbol{Q}_1 = \boldsymbol{Q}_2 = \cdots = \boldsymbol{Q}_K$ $t_1 \neq t_2 \neq \cdots \neq t_K$
     VE $\boldsymbol{Q}_1 \neq \boldsymbol{Q}_2 \neq \cdots \neq \boldsymbol{Q}_K$ $t_1 = t_2 = \cdots = t_K$
     VV $\boldsymbol{Q}_1 \neq \boldsymbol{Q}_2 \neq \cdots \neq \boldsymbol{Q}_K$ $t_1 \neq t_2 \neq \cdots \neq t_K$
Neighbor-Joining Method
Saitou, N. and Nei, M. 1987. "The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees." Molecular Biology and Evolution. 4:406--425.

Model-based Clustering

Rnd-EM
Maitra, R. 2007. "Initializing partition-optimization algorithms." IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6:114--157.
emEM
Biernacki, C. Celeux, G. and Govaert, G. 2003. "Choosing starting values for the EM algorithm for getting the highest likelihood in multivariate Gaussian mixture models." Computational Statistics and Data Analysis. 41:561--575.
ECM
Meng, X.-L. and Rubin, D.B. 1993. "Maximum Likelihood Estimation via the {ECM} Algorithm: A General Framework." Biometrika 80:267--278.
AECM
Meng, X.-L. and van Dyk, D. 1997. "The EM Algorithm --- an Old Folk-song Sung to a Fast New Tune (with discussion)." Journal of the Royal Statistical Society Series B. 59:511--567.

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Created: Nov 20 2009
Last Revised: Feb 13 2013, 12:16 (CDT Ames, IA, USA)
Maintained: Wei-Chen Chen
E-Mail: phyclust @ gmail.com

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