The haplotyping problem is a well-known problem in genomics, where the goal is to separate noisy sub-sequences obtained from slightly different sequences. This problem has many applications, for example to know precisely the species present in a microbiome.

We introduce a new modelisation of the problem as an integer linear programming problem, and a new implementation to solve the problem based on the use of the Gurobi solver. Though it is still in development, this approach has several key advantages compared to existing methods. In particular, it does not need as an input the number of haplotypes.