!!!Genome Analysis (4)

* [HMC]: Haplotype inference tool based on Markov Chain model
* [PTG]: Pasimonious tree-grow method for haplotype inference
* [LOHCRP]: LOH inference and segmentation tool based on conditional random field model
* [CKSAAP-Palm]: a tool for predicting palmitoylation sites from protein sequences


!!!Molecular Networks (9)

!!Gene Regulatory Networks Inference (2)

* [GNTInfer]: Gene network reconstruction tool with compound targets by integrating multiple microarray datasets and prior information 
* [GRNInfer]: Gene regulatory network inference tool from multiple microarray datasets 

!!PPI Networks Inference (3)

* [MDCInfer]: PPI prediction tool based on multiple domain cooperation analysis
* [DeterminePPI]: Inferring protein-protein interactions by parsimony principle 
* [InferPPI]: Predicting protein interactions based on parsimony tendency of domain interactions

!!Network Module Analysis (2)
* [PPICPM]: Identification of functional modules in PPI network by clique percolation clustering
* [ModularityOptimization]: Modularity optimization in community identification of complex networks

!!Network Alignment (2)
* [MNAligner]: Alignment of molecular networks by quadratic programming
* [PPINA]: Alignment of protein interaction networks by integer quadratic programming


!!!Structure Biology (4)

* [Samo]: Protein structure alignment tool based on multiple objective optimization
* [SANA]: Protein Structure Alignment by Neighborhood Alignment
* [StruComp]: Evaluating protein similarity from coarse structures
* [PSN]: Protein pocket similarity networks