Hypothesis Testing With Rank Conditions in Phylogenetics.

ABSTRACT: A phylogenetic model of sequence evolution for a set of n taxa is a collection of probability distributions on the 4 ⁿ possible site patterns that may be observed in their aligned DNA sequences. For a four-taxon model, one can arrange the entries of these probability distributions into three flattening matrices that correspond to the three different unrooted leaf-labeled four-leaf trees, or quartet trees. The flattening matrix corresponding to the tree parameter of the model is known to satisfy certain rank conditions. Methods such as ErikSVD and SVDQuartets take advantage of this observation by applying singular value decomposition to flattening matrices consisting of empirical data. Each possible quartet is assigned an "SVD score" based on how close the flattenin

SUBMITTER: Long C 

PROVIDER: S-EPMC8283673 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature