Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
for simulating data, additional analyses, and searching the best tree.

Description: Phylogenetic clustering (Phyloclustering) is a model-based
approach with the evolution theories and the Continuous Time
Markov Chain theory to identify population structures at the
molecular level without assuming linkage equilibrium. A finite
mixture model optimized by EM algorithms is implemented in C
with varied evolution models, identifiers, initializations and
optimizations. It also includes ms and seq-gen for generate
coalescent trees and sequences, and Hap-Clustering for SNP
sequences. See the phyclust website for more information,
Packaged: Thu Feb 18 08:07:04 2010; snoweye

"aut"), person("Yan-Han", "Chen", role = "ctb"))

coalescent trees and sequences, and incorporates Hap-Clustering
for SNP sequences. See the phyclust website for more
Packaged: Fri Feb 19 06:51:04 2010; snoweye

assuming linkage equilibrium. It provides a convenient
implementation of phyloclustering for DNA and SNP data, capable
of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It
is designed in C for performance, interfaced with R for
visualization, and incorporates other popular open source
software, ms, seq-gen and Hap-Clustering for simulating data
and additional analyses. See the phyclust website for more
Packaged: Sun Feb 21 00:08:44 2010; snoweye

Packaged: Sun Feb 21 23:28:48 2010; snoweye

Packaged: Fri Apr 9 14:11:46 2010; snoweye

Packaged: Mon Apr 26 01:28:24 2010; snoweye

Title: An extension of some of the classes in phylobase.  Tree objects
Depends: methods, phylobase (>= 0.6.2), ape (>= 2.5)
Description: This package enhancements to phylobase classes.  It
provides classes and methods which help uses manipulate
branch-annotated trees and provides supports for a few other

Title: An Extension (for Package 'SigTree') of Some of the Classes in
Imports: methods, phylobase, ape, grid, stats
Description: Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.