.identifier

Identifiers for evolution models identify the \(Q_k\) matrix and
 evolution time \(t_k\) for subpopulations.
 The first element is the default value.
 This is a read-only object and the elemental order is followed in C.

data

Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) 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 programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.

Wei-Chen Chen

phyclust

Phylogenetic Clustering (Phyloclustering)

Karin Dorman

.identifier function

A character vector contains implemented identifiers in C.

.identifier: Identifiers for Evolution Models

Description

Usage

Arguments

Format

Details

References

See Also

Examples