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PhyFoo: A software library based on JStacs to investigate phylogenetic footprinting

PhyFoo is a open source software library based on JStacs developed for investigating several aspects of phylogenetic footprinting. PhyFoo is extensively used during my PhD "Contributions to the understanding of gene regulation." Especially, PhyFoo was used to produce the results presented in the articles

• "Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information",
• "Unrealistic phylogenetic trees may improve phylogenetic footprinting", and
• "Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies". Advanced users should be able to use PhyFoo for de-novo motif prediction. Unfortunately, it is not very user-friendly yet.

The purpose of this wiki is to describe the usage of the single tools embedded in PhyFoo and to give readers of the above-mentioned articles the chance to repeat all tests and to recreate the results.