#### Phylogenetic Clustering
This website provides essential knowledge of
Phylogenetic Clustering
(Phyloclustering).
It provides implementations for studying phyloclustering:
- an R
package phyclust
available on
CRAN, and
- a C
library phyclust-c
which is the core of phyclust
.
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
- Wei-Chen Chen and
Karin S. Dorman.
---
#### 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
package phyclust
, please also cite
the corresponding references mentioned in the help pages of
phyclust
.
---