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.