.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

<p>See <code>all.internal</code> for phyclust.</p>
<p><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>.</p>

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.

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

Description

Arguments

References