Maximum Parsimony and the Skewness Test: A Simulation Study of the Limits of Applicability.

ABSTRACT: The maximum parsimony (MP) method for inferring phylogenies is widely used, but little is known about its limitations in non-asymptotic situations. This study employs large-scale computations with simulated phylogenetic data to estimate the probability that MP succeeds in finding the true phylogeny for up to twelve taxa and 256 characters. The set of candidate phylogenies are taken to be unrooted binary trees; for each simulated data set, the tree lengths of all (2n - 5)!! candidates are computed to evaluate quantities related to the performance of MP, such as the probability of finding the true phylogeny, the probability that the tree with the shortest length is unique, the probability that the true phylogeny has the shortest tree length, and the expected inverse of the number of trees sh

SUBMITTER: Maatta J 

PROVIDER: S-EPMC4818079 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature