This folder contains R package
The package is designed to detect Specificity Determining Sites (SDSs) in a multiple sequence alignment using a method of parsimony randomisation (Gilks and Wang, 2011).
The compressed file SDSparsimony_1.0-1.tar.gz contains the R code, documentation and some examples with data files.
To install the package:
to a directory of your choice.
- Install the package in R in one of the following ways:
- use the facilities provided in your R environment, or:
- get your system adminstrator to do it for you, or:
- if you have sufficient permissions and you have Rtools on your system, open a command tool window (Windows or Unix), change to the directory containing SDSparsimony_1.0-1.tar.gz, then type:
R CMD INSTALL -- clean SDSparsimony
- Start an R session and load the library by typing
from within your R session. Type
to get an overview of the package.
- The function which predicts SDS sites is called SDSpredict. Get help on using this function by typing
from within your R session.
28 March 2011
Gilks, W. and Wang, C. (2011) A Non-parametric Method for Detecting Specificity Determining Sites in
Protein Sequence Alignments. Statistical Applications in Genetics and Molecular Biology (in press).