Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

Phylogenetic inference and parsimony analysis.

On the Maximum Parsimony distance between phylogenetic trees

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the chara...

Bayesian Models for Phylogenetic trees

introduction: inferring genetic ancestry of different species is a current challenge in phylogenetics because of the immense raw biological data to be analyzed. computational techniques are necessary in order to parse and analyze all of such data in an efficient but accurate way, with many algorithms based on statistical principles designed to provide a best estimate of a phylogenetic topology....

Reduction rules for the maximum parsimony distance on phylogenetic trees

In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in tree inference, we recently introduced the maximum parsimony (MP) distance, which enjoys various attractive properties due to its connection with several other...

Searching for phylogenetic trees under the frequency parsimony criterion: an approximation using generalized parsimony.

Swofford and Berlocher (1987) described a method for inferring trees from polymorphic character data that searches for trees that minimize the total amount of allelic frequency change as measured by the Manhattan metric. We provided three primary arguments for choosing our method over other parsimony methods proposed for polymorphic data: (1) it accommodates polymorphism without resorting to co...