R

Summary: A statistical computing language and environment, similar in syntax and focus to the S language [Ross and Gentleman, 1996]. Mathematicians find R comparable to MATLAB. The BIOCONDUCTOR package for R provides support for bioinformatics [Gentleman et al., 2004]. Example: The following R code was used to produce Figure 3.1:

# Hardy—Weinberg curve p <- c(seq(0, 1, 0.001), seq(1, 100, 0.01)) z0 <- p~2/(1+p)~2 z1 <- 2*p/(1+p)"2 z2 <- 1/(1+p)"2

x.rec <- cbind((2*z0+z1)/sqrt(3), z1) ## plot the Hardy—Weinberg curve plot(x.rec[,1], x.rec[,2], type='l', xlim=c(0, 2/sqrt(3)), ylim=c(0, 1), xlab='', ylab='', yaxt='n', xaxt='n')

# plot simplex lines(x=c(0, 2/sqrt(3)), y=c(0, 0)) lines(x=c(0, 1/sqrt(3)), y=c(0, 1)) lines(x=c(1/sqrt(3), 2/sqrt(3)), y=c(1, 0))

Availability: Open source. Website: http://w¥w.r-project. org/

2.5.2 Computational biology software

The five software programs highlighted here were all used during the preparation of the book, and are mostly accessible through web servers.

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