Developing phylogenetic methods
(15 April 2009) These are notes for an ongoing project. Please let me know if you have suggestions.
-- Sam Riesenfeld
I am working on developing a phylogenetic method for metagenomic data. The basic idea is this:
* Build a reference tree with complete sequences. Iterate over the following two steps until all reads have been placed: * Place one read on the tree, hopefully using pplacer (see note below). * Re-estimate branch lengths and possibly topology using maximum likelihood (probably RAxML) for some portion of the tree containing the read just added.
Note: pplacer is a method developed by Erick Matsen while he was working with Robin Kodner. (See the summary of this method.) They haven't sent me a binary yet, though.
I'll add details as this develops. Right now it is really a rough idea.