I can't take any more of the tiny, unreadable posterior probability and bootstrap support values that I've been seeing on phylogenetic trees at the Ichs and Herps Meeting. Wouldn't it be easier to to put some easy-to-read symbols on the nodes instead of text in 4 point font? I understand why people haven't done this in the past -- it would have required individually replacing text with symbol at each node. Thanks to R, however, this tedious process is no longer necessary. Below are some simple instructions for doing this with posterior probability values included in the '.con' trees that are output from MrBayes using the sumt command (see further details in Paradis' book on R for phylogenetics). If you've never used R for phylogenetics before, you might also want to start at the new R-phylo Wiki.
#First, load the required library.
#Next, get your consensus tree from MrBayes into R.
read.nexus("your_file.con") -> your_tree
#Then, simplify matters by using only the tree with PP values.
your_tree[] -> your_tree
#Tell R to save the resulting tree file in PDF format.
#Generate the vector required to store values for background colors for symbols.
p <- character(length(your_tree$node.label))
#The following three lines define your labeling scheme. p[your_tree$node.label >= 0.95] <- "black"
p[your_tree$node.label < 0.95 & your_tree$node.label >= 0.75] <- "gray"
p[your_tree$node.label < 0.75] <- "white"
#Almost done, you're ready to plot your tree
#Now label your tree:'pch' tells R to use filled circles, 'cex' defines the size of the circles, and 'bg' tells it the name of the vector including the fill colors.
nodelabels(pch=21, cex = .75, bg = p)
#Finally, turn off the PDF writing
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