Multiple change-point recombination detection
Installation:
- Make sure you have the latest version of R. Among other dependencies, rbrothers relies on the rJava package, which in turn requires access to Java Development Kit (JDK). See rJava web page for more details.
- In R terminal, install dependencies by typing
install.packages(c("ape","rJava"))
- In R terminal, type
library(devtools)
install_github("vnminin/rbrothers",build_vignettes=TRUE)
Demos:
We provide the following scripts demonstrating the usage of the package.
- E. coli fimH (runs for about 2 minutes):
demo("fimH_example", package="rbrothers")
- Salmonella fimH and fimA (Warning: runs for a couple of hours, because MCMC was mixing poorly, so the number of iterations was bumped to 51 M):
demo("salmonella_example", package="rbrothers")
For a list of demos available in the package, type
demo(package="rbrothers")
If you want to copy and modify one of the demo R scripts, you can use the system.file() command to find the location of the script in your tree directory:
system.file("demo", "fimH_example.R", package="rbrothers")
References:
- Irvahn J, Chattopadhyay S, Sokurenko EV, Minin VN. rbrothers: R package for Bayesian multiple change-point recombination detection, Evolutionary Bioinformatics, 9, 235-238, 2013.
- Minin VN, Dorman KS, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection, Bioinformatics, 21, 3034-3042, 2005.
- Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS. Inferring spatial phylogenetic variation along nucleotide sequences: a multiple change-point model, Journal of the American Statistical Association, 98, 427-437, 2003.
- Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS. Oh brother, where art thou? a Bayes factor test for recombination with uncertain heritage, Systematic Biology, 51, 715-728, 2002.