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.

When mentioning the Phyloclustering methodology or the package phyclust, please cite:

Chen, W.-C. (2011), ``Overlapping Codon model, Phylogenetic Clustering, and Alternative Partial Expectation Conditional Maximization Algorithm,'' Ph.D. Diss., Iowa Stat University. 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.

Need Help

• Google Group: http://groups.google.com/group/phyclust
• Bugs Report: phyclust @ gmail.com

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.