Phyloclustering
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Section: Phyloclustering
What Is This?
This website provides essential knowledge of
Phylogenetic Clustering (Phyloclustering).It provides implementations for studying phyloclustering:
- an
R package phyclust available on
CRAN,
- a
C library phyclust-c
which is the core of phyclust, and
- a web interface
phyclust-php.
The phyclust
is an R package developed for studying phyloclustering
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 phyclust is designed in C for performance
and interfaced with R for visualization,
and sets up a common platform and
incorporates other popular open source software for
simulating data and additional analyses.
The phyclust
-
utilizes the R package
ape
(Paradis, Claude, and Strimmer 2004)
to present the concept of phyloclustering,
-
incorporates C program
ms (Hudson 2002)
for generating coalescent trees,
-
incorporates C program
seq-gen (Rambaut and Grassly 1997)
for simulating sequences,
-
incorporates C program
PAML baseml (Yang 1997,2007) for finding ancestral trees,
and
-
integrates R code
Hap-Clustering (Tzeng 2005)
an alternative method for SNP sequences.
Citation
When mentioning the Phyloclustering methodology or
the package phyclust, please cite:
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@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}
}
@MISC{chenphyclust,
author = {Chen, W.-C. and Dorman, K.},
title = {phyclust: Phylogenetic Clustering (Phyloclustering)},
year = {2010},
note = {R package, URL http://cran.r-project.org/package=phyclust}
}
This is a joint work with Drs. Karin S. Dorman, Ranja Maitra and
Susan L. Carpenter.
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When utilizing the incorporated C programs in the
package phyclust, please also cite
the corresponding references mentioned in the help pages of
phyclust.
Need Help
Authors
Wei-Chen Chen,
Karin S. Dorman, and
Ranjan Maitra.
Acknowledgment
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.
This website is built on a machine located in
the
Department of Statistics
at Iowa State University
in Ames
Iowa,
USA.
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