Eisen Lab Software

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 The following are published and unpublished projects that have software associated with them.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