Software

  • PhyloNet: A suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events, as well as inferring species trees despite lineage sorting.
  • PhyloNet-HMM: PhyloNet-HMM is a new statistical model and inference method for analyzing complex evolutionary scenarios, especially non-tree-like evolutionary scenarios, while accounting for within-genome dependencies.
  • TS2B: A tool for learning Boolean networks from time-series data.
  • NEPAL: A suite of software tools for reconstructing and analyzing phylogenetic networks under the maximum parsimony (MP) and maximum likelihood (ML) optimization criteria.
  • PathwayOracle: A suite of software tools for topology-based analyses of signal transduction networks.
  • GS2: A tool for computing the Gene Ontology (GO) based similarity of a set of genes.
  • Network Evolution: Tools for distance correction and ancenstral reconstruction for evolutionary analysis of molecular interaction networks.
  • Community Detection: Tools for community detection in metabolic networks (and networks in general). 
  • AGR: A tool that implements the Association Graph Reduction technique for detecting multi-locus genotype-phenotype association.
  • SimGE: A tool for simulating case/control data sets with various models of interacting markers.