We are not a software development lab, but we develop a lot of software tools to support our research and make it all available for anyone to use and repurpose. The following are published and unpublished projects that have software associated with them. We are in the process of making sure our legacy software is all available and has appropriate open source licenses attached. If you are looking for something that is not listed here, please contact us.
MacManes MD, Eisen MB (2013). Improving transcriptome assembly through error correction of high-throughput sequence reads.
Journal PubMed PMC Data:DRYAD Software:SCRIPTS
Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY et al. (2006). Large-scale turnover of functional transcription factor binding sites in Drosophila.
Journal PubMed PMC Software:CisEvolver
Pollard DA, Moses AM, Iyer VN, Eisen MB (2006). Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.
Journal PubMed PMC Software:CisEvolver
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB (2004). MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
Journal PubMed PMC Web Software:MONKEY
Moses AM, Chiang DY, Eisen MB (2004). Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.
PubMed Software:EMnEM
Gasch AP, Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering.
PubMed PMC Web Software:FuzzyK