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#### Useful Documents
The documents for the most stable version of <code>phyclust</code> is on
<a href="http://cran.r-project.org/web/packages/phyclust/index.html"
target="_blank">CRAN</a> or
<a href="http://cran.r-project.org/mirrors.html"
target="_blank">mirror sites</a>
from <a href="http://www.r-project.org"
target="_blnak">R-project</a>.
- The quick guide of <code>phyclust</code> (vignette):
[
<a href="./document/phyclust-guide.pdf"
target="_blank">pdf</a>
]
- The help pages of <code>phyclust</code> (manual):
[
<a href="./document/phyclust-help.pdf">pdf</a>
]
- The manual of <code>ms</code>
(<a href="http://home.uchicago.edu/~rhudson1/source/mksamples.html"
target="_blank">original source</a>):
[
<a href="./document/html/00Index.html"
target="_blank">html</a> |
<a href="./document/msdoc.pdf">pdf</a>
]
- The manual of <code>seq-gen</code>
(<a href="http://tree.bio.ed.ac.uk/software/seqgen/"
target="_blank">original source</a>):
[
<a href="./document/Seq-Gen.v.1.3.2/Seq-Gen.Manual.html"
target="_blank">html</a>
]
- The manual of <code>PAML baseml</code>
(<a href="http://abacus.gene.ucl.ac.uk/software/paml.html"
target="_blank">original source</a>):
[
<a href="./document/pamlDOC.pdf"
target="_blank">pdf</a>
]
---
#### Related References
Here are some references that are useful to understand
<code>phyclust</code> and <i>phyloclustering</i>.
- R and C:
* <i>R_note -- The Exploration of Statistical Software R</i>.
[
<a href="http://www.math.ncu.edu.tw/~chenwc/R_note/"
target="_blank">html</a>
]
* Chambers, J.M. (2008),
<i>Software for Data Analysis: Programming with R</i>, Springer.
* Davis, S.R. (1998), <i>C++ for Dummies</i>, 3rd, IDG Books Worldwide.
* Paradis, E. (2006),
<i>Analysis of Phylogenetics and Evolution with R</i>, Springer.
* Rudd, A. (1994), <i>Mastering C</i>, John Wiley and Sons.
* Venables and Ripley (2000), <i>S Programming</i>, Springer.
- Phylogenetics:
* Felsenstein, J. (2004), <i>Inferring Phylogenies</i>, Sinauer Associates.
* Graur, D. and Li, W.-H. (2000),
<i>Fundamentals of Molecular Evolution</i>, Sinauer Associates.
* Nielsen, R. (2005),
<i>Statistical Methods in Molecular Evolution</i>, Springer.
- Model-Based Clustering:
* Fraley, C. and Raftery, A.E. (2002),
"Model-Based Clustering, Discriminant Analysis, and Density Estimation",
<i>Journal of the American Statistical Association</i>,
<b>97</b>, 611-531.
* McLachlan, G.J. and Krishnan, T. (1996),
<i>The EM Algorithm and Extensions</i>, John Wiley and Sons.
* McLachlan, G.J. and Peel, D. (2000),
<i>Finite Mixture Models</i>, John Wiley and Sons.
- Virology:
* Goff, S., Coffin, J.M., Hugbes, S.H. and Varmus, H.E. (1997),
<i>Retroviruses</i>, Cold Spring Harbor Laboratory.
* Levy, J.A. (1992),
<i>The Retroviridae Volume 2</i>, Plenum.
- Haplotype Grouping:
* Thomas, D.C. (2004),
<i>Statistical Methods in Genetic Epidemiology</i>, Oxford.
* Tzeng, J.-Y. (2005),
"Evolutionary-Based Grouping of Haplotypes in Association Analysis",
<i>Genetics Epidemiology</i>, <b>28</b>, 220-231.
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