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Phyloclustering -- Phylogenetic Clustering
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:

  1. an R package phyclust available on CRAN,
  2. a C library phyclust-c which is the core of phyclust, and
  3. 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

  1. utilizes the R package ape (Paradis, Claude, and Strimmer 2004) to present the concept of phyloclustering,
  2. incorporates C program ms (Hudson 2002) for generating coalescent trees,
  3. incorporates C program seq-gen (Rambaut and Grassly 1997) for simulating sequences,
  4. incorporates C program PAML baseml (Yang 1997,2007) for finding ancestral trees, and
  5. 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:
    
@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.
When utilizing the incorporated C programs in the package phyclust, please also cite the corresponding references mentioned in the help pages of phyclust.

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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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Created: Nov 20 2009
Last Revised: May 08 2015, 06:20 (CDT Ames, IA, USA)
Maintained: Wei-Chen Chen
E-Mail: phyclust @ gmail.com
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