Phylogenetic Clustering
This website provides essential knowledge of Phylogenetic Clustering (Phyloclustering). It provides implementations for studying phyloclustering:
- an
R
packagephyclust
available on CRAN, and - a
C
libraryphyclust-c
which is the core ofphyclust
.
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.
Need Help
- Bugs Report: wccsnow @ gmail.com
Authors
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
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}, url = {http://gradworks.umi.com/34/73/3473002.html} }
- When utilizing the incorporated
C
programs in the packagephyclust
, please also cite the corresponding references mentioned in the help pages ofphyclust
.
Maintained: Wei-Chen Chen
E-Mail: wccsnow at gmail dot com
Last Updated: December 30, 2016
Created: November 20, 2009
E-Mail: wccsnow at gmail dot com
Last Updated: December 30, 2016
Created: November 20, 2009