About

This project contains a Clojure/Cascalog implementation for pruning phylogenetic trees. It rides on this algorithm for pre-processing trees so that they can be parallelized and pruned using MapReduce.

Running

You can run this from the shell:

hadoop jar phylotastic-0.1.0-SNAPSHOT-standalone.jar phylotastic.core.PruneTree /path/to/tol.csv /path/to/names.csv /tmp/results

Or by firing up the REPL:

(use `phylotastic.core)
(use `cascalog.api)
(tips->path "/path/to/tol.csv" "/path/to/names.csv" "/tmp/results")