bootstrap.merge.seq

bootstrap.star.tree

bootstrap.seq.nucleotide

bootstrap.seq.snp

check.EMC

check.label

convert.QA.to.vect

my.cat

my.format

my.print

plotfd

plothist.my

translate.EMC

translate.EMC.se

translate.ret

translate.ret.se

unstrsplit

code2nid.default

code2nid.list

nid2code.default

nid2code.list

code2snp.default

code2snp.list

snp2code.default

snp2code.list

sid2snp.default

sid2snp.list

snp2sid.default

snp2sid.list

nid2aid.default

nid2aid.list

nid2cid.default

nid2cid.list

cid2aid.default

cid2aid.list

aid2acode.default

aid2acode.list

acode2aid.default

acode2aid.list

See <code>all.internal.tzeng</code> for Tzeng's methods (2005).
The following are all internal functions: 
 <code>bootstrap.merge.seq</code>,
 <code>bootstrap.star.tree</code>, 
 <code>bootstrap.seq.nucleotide</code>,
 <code>bootstrap.seq.snp</code>, 
 <code>check.EMC</code>,
 <code>check.label</code>,
 <code>convert.QA.to.vect</code>, 
 <code>my.cat</code>,
 <code>my.format</code>, 
 <code>my.print</code>,
 <code>plotfd</code>, 
 <code>plothist.my</code>,
 <code>translate.EMC</code>, 
 <code>translate.ret</code>,
 <code>unstrsplit</code>.
The following are all S3 methods: 
 <code>code2nid.default</code>,
 <code>code2nid.list</code>, 
 <code>nid2code.default</code>,
 <code>nid2code.list</code>, 
 <code>code2snp.default</code>,
 <code>code2snp.list</code>, 
 <code>snp2code.default</code>,
 <code>snp2code.list</code>, 
 <code>sid2snp.default</code>,
 <code>sid2snp.list</code>, 
 <code>snp2sid.default</code>,
 <code>snp2sid.list</code>, 
 <code>nid2aid.default</code>,
 <code>nid2aid.list</code>, 
 <code>nid2cid.default</code>,
 <code>nid2cid.list</code>, 
 <code>cid2aid.default</code>,
 <code>cid2aid.list</code>, 
 <code>aid2acode.default</code>,
 <code>aid2acode.list</code>, 
 <code>acode2aid.default</code>,
 <code>acode2aid.list</code>.

internal

all.internal

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: All Internal Functions of phyclust

Description

Arguments

References