These proceedings contain papers from the 2009 Workshop on Algorithms in Bioinformatics (WABI)
held at the University of Pennsylvania in Philadelphia Pennsylvania during September 12-13
2009. WABI 2009 was the ninth annual conference in this series which focuses on novel
algorithms that address imp- tantproblemsingenomics molecularbiology
andevolution.Theconference- phasizes research that describes computationally e?cient algorithms
and data structures that have been implemented and tested in simulations and on real data. WABI
is sponsored by the European Association for Theoretical C- puter Science (EATCS) and the
International Society for Computational Bi- ogy (ISCB). WABI 2009 was supported by the Penn
Genome Frontiers Institute and the Penn Center for Bioinformatics at the University of
Pennsylvania. For the 2009 conference 90 full papers were submitted for review by the Program
Committee and from this strong ?eld of submissions 34 papers were chosen for presentation at
the conference and publication in the proceedings. The ?nal programcovered a wide range of
topics including gene interaction n- works molecular phylogeny RNA and protein structure and
genome evolution.
