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#### Phylogenetic Clustering
This website provides essential knowledge of
<a href="./overview.html"><i>Phylogenetic Clustering</i></a>
(<i>Phyloclustering</i>).
It provides implementations for studying <i>phyloclustering</i>:
- an <code>R</code> package <code><b>phyclust</b></code> available on
<a href="http://cran.r-project.org/web/packages/phyclust/index.html"
target="_blank">CRAN</a>, and
- a <code>C</code> library <code><b>phyclust-c</b></code>
which is the core of <code><b>phyclust</b></code>.
The <code><b>phyclust</b></code>
is an <code>R</code> package developed for studying <i>phyloclustering</i>
and exploring population structure of DNA sequence data.
An evolutionary Continuous Time Markov Chain model-based approach
is developed to determine population structure from molecular data
without assuming linkage equilibrium.
The <code>phyclust</code> is designed in <code>C</code> for performance
and interfaced with <code>R</code> for visualization,
and sets up a common platform and
incorporates other popular open source software for
simulating data and additional analyses.
The <code>phyclust</code>
- utilizes the R package
<a href="http://ape.mpl.ird.fr/" target="_blank"><code>ape</code></a>
(Paradis, Claude, and Strimmer 2004)
to present the concept of <i>phyloclustering</i>,
- incorporates C program
<a href="http://home.uchicago.edu/~rhudson1/source/mksamples.html"
target="_blank"><code>ms</code></a> (Hudson 2002)
for generating coalescent trees,
- incorporates C program
<a href="http://tree.bio.ed.ac.uk/software/seqgen/"
target="_blank"><code>seq-gen</code></a> (Rambaut and Grassly 1997)
for simulating sequences,
- incorporates C program
<a href="http://abacus.gene.ucl.ac.uk/software/paml.html"
target="_blank"><code>PAML baseml</code></a> (Yang 1997,2007)
for finding ancestral trees, and
- integrates R code
<a href="http://www4.stat.ncsu.edu/~jytzeng/software.php"
target="_blank"><code>Hap-Clustering</code></a> (Tzeng 2005)
an alternative method for SNP sequences.
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#### Need Help
- Bugs Report:
<a href="mailto:wccsnow @ gmail.com">wccsnow @ gmail.com</a>
---
#### Authors
- <a href="http://snoweye.github.io" target="_blank"> Wei-Chen Chen</a> and
<a href="http://thirteen-01.stat.iastate.edu/"
target="_blank">Karin S. Dorman</a>.
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#### Acknowledgement
- This is a joint work with Drs. Karin S. Dorman, Ranja Maitra and
Susan L. Carpenter.
- Wei-Chen thanks Drs. Dorman and Maitra of Iowa State University for helpful
discussion, and is a research assistant on grant
National Science Foundation CAREER # DMS-0437555.
---
#### Citation
- When mentioning the Phyloclustering methodology or
the package <code>phyclust</code>, please cite:
```
@ARTICLE{snoweye2011,
author = {Chen, W.-C.},
title = {Overlapping Codon model, Phylogenetic
Cluetering, and Alternative Partial Expectation
Conditional Maximization Algorithm},
journal = {Ph.D. Diss., Iowa Stat University},
year = {2011},
url = {http://gradworks.umi.com/34/73/3473002.html}
}
```
- When utilizing the incorporated <code>C</code> programs in the
package <code>phyclust</code>, please also cite
the corresponding references mentioned in the help pages of
<code>phyclust</code>.
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