Before revision:  We give a linear time algorithm and a parameterized near linear time algorithm to construct a repeat-free founder graph and a repeat-free elastic founder graph, respectively.
After revision:  We give a linear time algorithm and a parameterized near linear time algorithm to construct a repeat-free non-elastic founder graph from a gapless MSA, and (parameterized) near-linear time algorithms to construct semi-repeat-free ( repeat-free elastic founder graph, respectively.