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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

# plot trees of three methods together,
# with nodes with age estimates labeled
layout(matrix(1:3, 1, 3))
plot(trees_out[[1]])
nodelabels(trees_out[[1]]$node.label, cex = 0.6) title("original tree") plot(trees_out[[2]]) nodelabels(trees_out[[2]]$node.label, cex = 0.6)
plot(trees_out[[3]])
nodelabels(trees_out[[3]]\$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.