A Simple Phylogenetic Branch Length Adjuster
PurposeWhat do you do if you have a phylogenetic topology, with some nodes aged, but no branch lengths to smooth the rates of (with r8s)? You can still use r8s without branch lengths to force an ultrametric tree. Or you can use BLADJ!
This is a simple utility that takes a phylogeny, fixes the root node at a specified age, and fixes other nodes you might have age estimates for. It then sets all other branch lengths by placing the nodes evenly between dated nodes, and between dated nodes and terminals (of age 0). This has the effect of minimizing variance in branch length, within the constraints of dated nodes. It thus produces a pseudo-chronogram that can be useful for estimating phylogenetic distance (in units of time) between taxa for, for instance, the analysis of community phylogenetic structure. Even with only a few nodes dated, the resulting phylogenetic distances can be a marked improvement on simply using the number of intervening nodes as a phylogenetic distance (see Webb 2000).
The applicationBladj takes as its input a phylogeny (named 'phylo' in newick format), with named internal nodes, and a simple table of interior node names and ages. It returns a new phylogeny with adjusted branch lengths. Note that the root node must be named and given an age. Utilities included in the distribution allow conversion between Newick and Nexus files and the .fy format. Bladj is C-code that can be compiled on any platform. An executable for Mac OS X Darwin is included.
Included in the distribution is a simple ages file (called 'ages') with angiosperm nodes aged according to Wikstrom et al. (2001). I fully acknowledge that these ages are not the maximum age for, e.g. a family, but simply an estimate of the MRCA of the two most distant taxa in a clade included in Wikstrom's analysis. The correct statement is that the clade represented by this node is at least as old as the age given, and no older than the age of the next older node dated in the list. We all await an online database of fossil-based estimates of node age!
Feel free to DOWNLOAD bladj (now incorporated in phylocom). Please send comments and bug reports to Cam Webb. This utility is a companion to phylomatic and phylocom.