README

EDO is a tool for selecting Ensemble-Diversity Optimised hairpins used as
barcodes in the context of high throughput synthesis pipelines, like Cloud Lab
(see http://daslab.stanford.edu/das_research.html)

Partition functions are computed using the ViennaRNA package.
http://www.tbi.univie.ac.at/RNA/

The distributed auction algorithm is largely based on ideas presented in
  Zavlanos, M.M.; Spesivtsev, L.; Pappas, G.J., 
  "A distributed auction algorithm for the assignment problem,"
  47th IEEE Conference on Decision and Control, 2008. CDC 2008.
  pp.1212-1217, 9-11 Dec. 2008
which can be found online at 
  http://dx.doi.org/10.1109/CDC.2008.4739098
  or http://repository.upenn.edu/grasp_papers/33/


Build the usual way:

  ./configure
  make

and then try

  src/edo -v < data/r89f.list >data/r89f.seqs
  src/edo --eval < data/r89f.seqs