Some terminologies used in <code>phyclust</code> 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 $K$ clusters <table> <thead> <tr align="center"> <th bgcolor="#d3dce3"> Identifier </th> <th bgcolor="#d3dce3"> $\boldsymbol{Q}$ </th> <th bgcolor="#d3dce3"> $t$ </th> </tr> </thead> <tbody> <tr align="center"> <td bgcolor="#dddddd"> <code>EE</code> </td> <td bgcolor="#dddddd"> $\boldsymbol{Q}\_1 = \boldsymbol{Q}\_2 = \cdots = \boldsymbol{Q}\_K$ </td> <td bgcolor="#dddddd"> $t\_1 = t\_2 = \cdots = t\_K$ </td> </tr> <tr align="center"> <td bgcolor="#cccccc"> <code>EV</code> </td> <td bgcolor="#cccccc"> $\boldsymbol{Q}\_1 = \boldsymbol{Q}\_2 = \cdots = \boldsymbol{Q}\_K$ </td> <td bgcolor="#cccccc"> $t\_1 \neq t\_2 \neq \cdots \neq t\_K$ </td> </tr> <tr align="center"> <td bgcolor="#dddddd"> <code>VE</code> </td> <td bgcolor="#dddddd"> $\boldsymbol{Q}_1 \neq \boldsymbol{Q}\_2 \neq \cdots \neq \boldsymbol{Q}\_K$ </td> <td bgcolor="#dddddd"> $t\_1 = t\_2 = \cdots = t\_K$ </td> </tr> <tr align="center"> <td bgcolor="#cccccc"> <code>VV</code> </td> <td bgcolor="#cccccc"> $\boldsymbol{Q}_1 \neq \boldsymbol{Q}\_2 \neq \cdots \neq \boldsymbol{Q}\_K$ </td> <td bgcolor="#cccccc"> $t\_1 \neq t\_2 \neq \cdots \neq t\_K$ </td> </tr> </tbody> </table> - 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. --- <div w3-include-html="./preamble_tail_date.html"></div>