Fast algorithms for inferring evolutionary trees.
We present algorithms for the perfect phylogeny problem restricted to binary characters. The first algorithm is faster than a previous algorithm by Gusfield when the input matrix for the problem is sparse. Next, we present two online algorithms. For the first of these, the set of species is fixed and the characters are given as input one at a time, while, for the second, the set of characters is fixed and the species are given as input one at a time. These two online algorithms are then combined into an algorithm that can process any sequence of additions and deletions of species and characters.
Agarwala
R
R
DIMACS (Center for Discrete Mathematics and Theoretical Computer Science), Rutgers University, Piscataway, NJ 08855, USA.
Fernández-Baca
D
D
Slutzki
G
G
D000465:Algorithms; D005075:Biological Evolution; D009862:Online Systems; D010802:Phylogeny