Useful Documents
The documents for the most stable version of phyclust
is on
CRAN or
mirror sites
from R-project.
The quick guide of
phyclust
(vignette): [ pdf ]The help pages of
phyclust
(manual): [ pdf ]The manual of
ms
(original source): [ html | pdf ]The manual of
seq-gen
(original source): [ html ]The manual of
PAML baseml
(original source): [ pdf ]
Related References
Here are some references that are useful to understand
phyclust
and phyloclustering.
- R and C:
- R_note -- The Exploration of Statistical Software R. [ html ]
- Chambers, J.M. (2008), Software for Data Analysis: Programming with R, Springer.
- Davis, S.R. (1998), C++ for Dummies, 3rd, IDG Books Worldwide.
- Paradis, E. (2006), Analysis of Phylogenetics and Evolution with R, Springer.
- Rudd, A. (1994), Mastering C, John Wiley and Sons.
- Venables and Ripley (2000), S Programming, Springer.
- Phylogenetics:
- Felsenstein, J. (2004), Inferring Phylogenies, Sinauer Associates.
- Graur, D. and Li, W.-H. (2000), Fundamentals of Molecular Evolution, Sinauer Associates.
- Nielsen, R. (2005), Statistical Methods in Molecular Evolution, Springer.
- Model-Based Clustering:
- Fraley, C. and Raftery, A.E. (2002), "Model-Based Clustering, Discriminant Analysis, and Density Estimation", Journal of the American Statistical Association, 97, 611-531.
- McLachlan, G.J. and Krishnan, T. (1996), The EM Algorithm and Extensions, John Wiley and Sons.
- McLachlan, G.J. and Peel, D. (2000), Finite Mixture Models, John Wiley and Sons.
- Virology:
- Goff, S., Coffin, J.M., Hugbes, S.H. and Varmus, H.E. (1997), Retroviruses, Cold Spring Harbor Laboratory.
- Levy, J.A. (1992), The Retroviridae Volume 2, Plenum.
- Haplotype Grouping:
- Thomas, D.C. (2004), Statistical Methods in Genetic Epidemiology, Oxford.
- Tzeng, J.-Y. (2005), "Evolutionary-Based Grouping of Haplotypes in Association Analysis", Genetics Epidemiology, 28, 220-231.