Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.
Get the code and example files here: http://wp.me/PRT1F-2v
Get phylocom here: http://www.phylodiversity.net/phylocom/
The code uses as input a newick tree file and a text file of node ages.
# This is where the work happens... # Directory below needs to have at least three items: # 1. phylocom executable for windows or mac # 2. tree newick file # 3. node ages file as required by phylocom, see their manual # Output: trees_out is a list of three trees, the original, bladj, and Gene Hunt's method # Also, within the function all three trees are written to file as PDFs setwd("/Mac/R_stuff/Blog_etc/Bladjing") trees_out <- AdjBrLens("tree.txt", "nodeages.txt") # plot trees of three methods together, # with nodes with age estimates labeled layout(matrix(1:3, 1, 3)) plot(trees_out[]) nodelabels(trees_out[]$node.label, cex = 0.6) title("original tree") plot(trees_out[]) nodelabels(trees_out[]$node.label, cex = 0.6) title("bladj method") plot(trees_out[]) nodelabels(trees_out[]$node.label, cex = 0.6) title("gene hunt method, scalePhylo")
It is sort of hard to see the differences in the branch length changes here, but the individual output trees will reveal the differences better.