mlegp: statistical analysis for computer models of biological systems using R

This is a test. cBrother A program written in C to infer rare recombination events from aligned nucleotide sequence data. Suchard et. al developed a Bayesian multiple change point model to test for the presence of rare recombination events in the history of a set of sampled sequences Suchard02a Suchard03a . In this model, an unknown number of evolutionary change points, where mutation rates or topology change, were hypothesized to occur throughout the alignment. Later, Minin et. al separated the evolutionary change point process into two separate processes, one describing the topological changes along an alignment, and another describing the changes in rates Minin05a The original Java version of the software for running these models is available on Marc Suchard's website. cBrother is a C version of the Java code with a few changes. In particular, the C version implements additional priors for testing whether recombinant sequences with similar structure resulted from a single or multiple recombination events. Please see the cBrother Wiki for more information. NA Linux|Mac|Windows tar gzip http://rumi.gdcb.iastate.edu/wiki/cBrother 2006-09-15 Version 2.0 108 KB Linux tar gzip cbrother1.0.tar.gz 2005-05-07 Version 1.0 Suchard02a Suchard03a Minin05a efron A program written in C to estimate the p-value in support of a hypothesis of recombination among aligned nucleotide sequence data. Dorman et. al developed a corrected bootstrap procedure for testing recombination hypotheses Dorman02 . More to come. 88 KB Linux tar gzipped efron1.0.tar.gz 2005-05-07 Original public release 88 KB Linux tar gzipped efron1.1.tar.gz 2005-09-21 Fixes bugs to work with newer linux distributions Dorman01 Dorman02 mlegp An R package to analyze computer models of complex systems. Gaussian processes (GPs) are flexible statistical models commonly used for predicting output from complex computer codes. As such, GPs are well-suited for the analysis of computer models of biological systems, which have been traditionally difficult to analyze due to their high-dimensional, non-linear, and resource-intensive nature. We describe an R package, mlegp, that fits GPs to computer model outputs and performs sensitivity analysis to identify and characterize the effects of important model parameters. Go to mlegp's CRAN page to download the package. Dancik07a Dancik07b Suchard MA Weiss RE Dancik GM Dorman KS Jones DE Minin VN Sinsheimer JS Fang F Kaplan AH DancikGM DormanKS 2007 mlegp: statistical analysis for computer models of biological systems using R Bioinformatics Bioinformatics Submitted DancikGM JonesDE DormanKS 2007 Parameter estimation and sensitivity analysis in an agent-based model of Leishmania major infection Journal of Theoretical Biology J. Theor. Biol. In progress SuchardMA WeissRE DormanKS SinsheimerJS 2002 Oh brother where art thou? A bayes factor test for recombination with uncertain heritage Systematic Biology Syst. Biol. 51 5 1 14 Published SuchardMA WeissRE DormanKS SinsheimerJS 2003 Inferring spatial phylogenetic variation along nucleotide sequences Journal of the American Statistical Association J. Am. Stat. Assoc. 98 427 437 Published MininVN DormanKS FangF SuchardMA 2005 Dual multiple change-point model leads to more accurate recombination detection Bioinformatics In press DormanKS 2001 Dissertation: Human Immunodeficiency Virus Type 1 Genome Variability - Recombination and Emergence of Resistance UCLA DormanKS KaplanAH SinsheimerJS 2002 Bootstrap confidence levels for HIV-1 recombination Journal of Molecular Evolution J. Mol. Evol. 54 2 200 209 Published