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| sidier-package | SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships |
| BARRIEL | Indel distances following Barriel method |
| distance.comb | Distance matrices combiantion |
| FIFTH | Indel distances following the fifth state rationale |
| FindHaplo | Find equal haplotypes |
| GetHaplo | Get sequences of unique haplotypes |
| HapPerPop | Returns the number of haplotypes per population. |
| MCIC | Modified Complex Indel Coding as distance matrix |
| mutationSummary | Summary of observed mutations |
| nt.gap.comb | substitution and indel distance combinations |
| perc.thr | Percolation threshold network |
| pop.dist | Distances among populations |
| SIC | Indel distances following the Simple Index Coding method |
| sidier | SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships |
| simuEvolution | Simulate sequences evolution |
| single.network | Plot a network given a threshold |