Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Reconstructing a history of recombinations from a set of sequences
SODA '94 Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms
Fixed topology alignment with recombination
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
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Let Σ be an alphabet and Σn denote the collection of all sequences of length n over Σ. For any s1 = ajaj+1 . . . an+s2 = b1b2 . . . bj bj+1 . . . bn ∈ Σn, a recombination of s1 and s2 at position j is defined as an operation that crosses s1 and s2 at position j and generates t1 = a1a2 . . . ajbj+1 . . . bn and t2 = b1b2 . . . bjaj+1 . . . an. Denote A and S two collections of sequences. In this paper, we discuss generating A from S by a series of recombinations in minimum number of steps. We present a greedy algorithm for finding the optimal recombination evolutionary history from S to any tree A of sequences when |S| = 2.