Constructing a Fully Ranked phylogenetic Constraint Tree using Monophyletic Group, Crown Group and Relative Age Constraints

Abstract

Phylogenetic research field concerned with the reconstructing of the phylogenetic tree using some information that has evolved from the root to all the descendants. There are many ways to try and find the best tree.If one knows beforehand that a subset of species form a subgroup that are closely related then one can constrain the search algorithm to only look for those trees where this subset of species forms a subtree. Placing such constraints reduces the number of trees that the search algorithm must consider and thus reduces the time spent searching for the best tree. In Bayesian phylogenetic inference we are interested in distributions over a space of trees. When fossil evidence is used in the inference to constrain the tree, new tree spaces arise and counting the number of trees is more difficult. We have constructed a tree using algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is three.