#### Phylogenetic Clustering This website provides essential knowledge of <a href="./overview.html"><i>Phylogenetic Clustering</i></a> (<i>Phyloclustering</i>). It provides implementations for studying <i>phyloclustering</i>: - an <code>R</code> package <code><b>phyclust</b></code> available on <a href="http://cran.r-project.org/web/packages/phyclust/index.html" target="_blank">CRAN</a>, and - a <code>C</code> library <code><b>phyclust-c</b></code> which is the core of <code><b>phyclust</b></code>. The <code><b>phyclust</b></code> is an <code>R</code> package developed for studying <i>phyloclustering</i> 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 <code>phyclust</code> is designed in <code>C</code> for performance and interfaced with <code>R</code> for visualization, and sets up a common platform and incorporates other popular open source software for simulating data and additional analyses. The <code>phyclust</code> - utilizes the R package <a href="http://ape.mpl.ird.fr/" target="_blank"><code>ape</code></a> (Paradis, Claude, and Strimmer 2004) to present the concept of <i>phyloclustering</i>, - incorporates C program <a href="http://home.uchicago.edu/~rhudson1/source/mksamples.html" target="_blank"><code>ms</code></a> (Hudson 2002) for generating coalescent trees, - incorporates C program <a href="http://tree.bio.ed.ac.uk/software/seqgen/" target="_blank"><code>seq-gen</code></a> (Rambaut and Grassly 1997) for simulating sequences, - incorporates C program <a href="http://abacus.gene.ucl.ac.uk/software/paml.html" target="_blank"><code>PAML baseml</code></a> (Yang 1997,2007) for finding ancestral trees, and - integrates R code <a href="http://www4.stat.ncsu.edu/~jytzeng/software.php" target="_blank"><code>Hap-Clustering</code></a> (Tzeng 2005) an alternative method for SNP sequences. --- #### Need Help - Bugs Report: <a href="mailto:wccsnow @ gmail.com">wccsnow @ gmail.com</a> --- #### Authors - <a href="http://snoweye.github.io" target="_blank"> Wei-Chen Chen</a> and <a href="http://thirteen-01.stat.iastate.edu/" target="_blank">Karin S. Dorman</a>. --- #### Acknowledgement - This is a joint work with Drs. Karin S. Dorman, Ranja Maitra and Susan L. Carpenter. - 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. --- #### Citation - When mentioning the Phyloclustering methodology or the package <code>phyclust</code>, 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}, url = {http://gradworks.umi.com/34/73/3473002.html} } ``` - When utilizing the incorporated <code>C</code> programs in the package <code>phyclust</code>, please also cite the corresponding references mentioned in the help pages of <code>phyclust</code>. --- <div w3-include-html="./preamble_tail_date.html"></div>