Gaphyl

Gaphyl: A genetic algorithms approach to cladistics. This research investigates the use of genetic algorithms to solve problems from cladistics - a technique used by biologists to hypothesize the evolutionary relationships between organisms. Since exhaustive search is not practical in this domain, typical cladistics software packages use heuristic search methods to navigate through the space of possible trees in an attempt to find one or more “best” solutions. We have developed a system called Gaphyl, which uses the genetic algorithm approach as a search technique for finding cladograms, and a tree evaluation metric from a common cladistics software package (Phylip). On a nontrivial problem (49 species with 61 attributes), Gaphyl is able to find more of the best known trees with less computational effort than Phylip is able to find (corresponding to more equally plausible evolutionary hypotheses).

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