The kernel part of the package are implemented in C.
EM algorithms are performed to find the maximum likelihood estimators.
Initialization methods for EM algorithms are also established.
Several evolution models are also developed.
ms and seq-gen are two useful programs to generate
coalescent trees and sequences, and both are merged into
Type help(package = phyclust) to see a list of major
functions for which further documentations are available. The on-line
detail instructions are also available and the link is given below in the
Some C and R functions and R classes of the
phyclust controlled by an object
.EMC generated by a function .EMControl,
and find.best can find the best solution by repeating
phyclust with different initializations. ms and seqgen can generate trees and sequences
based on varied conditions, and they can jointly perform simulations.
haplo.post.prob is a modified version of Tzeng's method
for haplotype grouping which uses a evolution approach to group SNP
sequences.
Some tool functions of the
Hudson, R.R. (2002)
Rambaut, A. and Grassly, N.C. (1997)
Tzeng, J.Y. (2005)
Paradis E., Claude J., and Strimmer K. (2004)
phyclust,
.EMC,
.EMControl,
find.best.demo(package = "phyclust")
demo("ex_trees", package = "phyclust")Run the code above in your browser using DataLab