Lists of Software#

1. CKSAAP-Palm
2. DeterminePPI
3. GNTInfer
4. GRNInfer
5. HMC
6. InferPPI
7. LOHCRP
8. MDCInfer
9. MNAligner
10. ModularityOptimization
11. PPICPM
12. PPINA
13. PSN
14. PTG
15. PTMPred
16. Samo
17. SANA
18. StruComp

Genome Analysis (5)#

• 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
• PTMPred: a tool for predicting post-transcriptional modification 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