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| AlignedPairs | Get aligned node pairs |
| AlignNetworks | Align networks |
| AnalyzeAlignment | Analyze an alignment |
| ComputeLinkParameters | Compute link parameters |
| ComputeM | Compute score matrix M |
| ComputeNodeParameters | Compute node parameters |
| ComputeScores | Compute scores |
| CreateScoreMatrix | Create score matrix |
| EncodeDirectedGraph | Encode directed graph |
| GenerateExample | Generate example input data |
| GetBinNumber | Get bin number |
| InitialAlignment | Create initial alignment |
| InvertPermutation | Invert permutation |
| LinearAssignment | Solve linear assignment problem |
| MatrixToBin | Convert matrix to bin representation |
| Permute | Permute rows and columns of a matrix |
| Trace | Calculate trace of a matrix |
| VectorToBin | Convert vector to bin representation |