IRiS produces a subARG in two phases by given a collection of haplotypes. A combinatorial algorithm called the DSR is a model-based approach to detecting recombinations in haplotypes (with a guaranteed approximation factor). The algorithm is based on iteratively classifying sets of lineages as dominant, subdominant or recombinant (DSR). In the first phase, DSR is run multiple times with different sets of parameters and statistical consensus is derived from them to produce a matrix of recombination information called the recomatrix. This encodes the local topology information of only the high confidence recombination events detected in the first phase. The subARG is constructed from the recomatrix in the second phase
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Javed, A., Pybus, M., Melé, M., Utro, F., Bertranpetit, J., Calafell, F., and Parida, L.,
IRiS: Construction of ARG network at genomic scales,
Bioinformatics (2011) 27 (17): 2448-2450.