.tzengEnv

chkdim.Add.fun

chkdim.Multiply.fun

construct.bigB.dPI

construct.dB.list.fun

final.BigMatB.fun

final.BigMatB.matC.fun

get.allpossROUTE.fun

get.BB.fun

get.deriBigMatB.fun

get.fullBB.fun

get.I.fun

get.ini.possHap.hapReserv.fun

get.medBB.skip.fun

get.preBB.skip.fun

get.step.mut.fun

get.subPI.fun

getBigMatB.fun

getI13.fun

getPIstar.fun

haplo.phase.known

I33Inv.fun

index.k.fun

zero.mat.fun

See <code>all.internal</code> for phyclust.
<code>chkdim.Add.fun</code>,
 <code>chkdim.Multiply.fun</code>, 
 <code>construct.bigB.dPI</code>,
 <code>construct.dB.list.fun</code>, 
 <code>final.BigMatB.fun</code>,
 <code>final.BigMatB.matC.fun</code>, 
 <code>get.allpossROUTE.fun</code>,
 <code>get.BB.fun</code>, 
 <code>get.deriBigMatB.fun</code>,
 <code>get.fullBB.fun</code>, 
 <code>get.I.fun</code>,
 <code>get.ini.possHap.hapReserv.fun</code>, 
 <code>get.medBB.skip.fun</code>, 
 <code>get.preBB.skip.fun</code>,
 <code>get.step.mut.fun</code>, 
 <code>get.subPI.fun</code>,
 <code>getBigMatB.fun</code>, 
 <code>getI13.fun</code>,
 <code>getPIstar.fun</code>, 
 <code>haplo.phase.known</code>,
 <code>I33Inv.fun</code>,
 <code>index.k.fun</code>, 
 <code>zero.mat.fun</code>.

internal

Haploclust

all.internal.tzeng

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

Yan-Han Chen

all.internal.tzeng function

Jung-Ying Tzeng
Maintain: Wei-Chen Chen <a href="/link/wccsnow%40gmail.com?package=phyclust&version=0.1-34" data-mini-rdoc="phyclust::wccsnow@gmail.com">wccsnow@gmail.com</a>

Author

See <code>all.internal</code> for phyclust.
<code>chkdim.Add.fun</code>,
 <code>chkdim.Multiply.fun</code>, 
 <code>construct.bigB.dPI</code>,
 <code>construct.dB.list.fun</code>, 
 <code>final.BigMatB.fun</code>,
 <code>final.BigMatB.matC.fun</code>, 
 <code>get.allpossROUTE.fun</code>,
 <code>get.BB.fun</code>, 
 <code>get.deriBigMatB.fun</code>,
 <code>get.fullBB.fun</code>, 
 <code>get.I.fun</code>,
 <code>get.ini.possHap.hapReserv.fun</code>, 
 <code>get.medBB.skip.fun</code>, 
 <code>get.preBB.skip.fun</code>,
 <code>get.step.mut.fun</code>, 
 <code>get.subPI.fun</code>,
 <code>getBigMatB.fun</code>, 
 <code>getI13.fun</code>,
 <code>getPIstar.fun</code>, 
 <code>haplo.phase.known</code>,
 <code>I33Inv.fun</code>,
 <code>index.k.fun</code>, 
 <code>zero.mat.fun</code>.

All Internal Functions of Tzeng's Methods — all.internal.tzeng

Jung-Ying Tzeng
Maintain: Wei-Chen Chen <a href='mailto:wccsnow@gmail.com'>wccsnow@gmail.com</a>

All Internal Functions of Tzeng's Methods

all.internal.tzeng: All Internal Functions of Tzeng's Methods

Description

Arguments

Author

References