library(ape) ### ### Chapter 3 ### x <- paste("AY66", 6597:7060, sep = "") x <- c(x, "AY724411", "AY724412") astraptes.seq <- read.GenBank(x) table(sapply(astraptes.seq, length)) astraptes.seq.ali <- clustal(astraptes.seq) table(attr(astraptes.seq, "species")) taxa.astraptes <- attr(astraptes.seq, "species") names(taxa.astraptes) <- names(astraptes.seq) save(astraptes.seq.ali, taxa.astraptes, file = "astraptes.RData") ### ### Chapter 5 ### M.astraptes.K80 <- dist.dna(astraptes.seq.ali, p = TRUE) summary(M.astraptes.K80) hist(M.astraptes.K80) tr <- nj(M.astraptes.K80) tr$tip.label <- taxa.astraptes[tr$tip.label] taxon <- unique(taxa.astraptes) L <- vector(mode = "list", length = 10) for (i in 1:10) L[[i]] <- grep(taxon[i], tr$tip.label) zoom(tr, L)