Combining distance matrices on identical taxon sets for multi-gene analysis with singular value decomposition.

ABSTRACT: We present a simple and effective method for combining distance matrices from multiple genes on identical taxon sets to obtain a single representative distance matrix from which to derive a combined-gene phylogenetic tree. The method applies singular value decomposition (SVD) to extract the greatest common signal present in the distances obtained from each gene. The first right eigenvector of the SVD, which corresponds to a weighted average of the distance matrices of all genes, can thus be used to derive a representative tree from multiple genes. We apply our method to three well known data sets and estimate the uncertainty using bootstrap methods. Our results show that this method works well for these three data sets and that the uncertainty in these estimates is small. A simulation stud

SUBMITTER: Abeysundera M 

PROVIDER: S-EPMC3986248 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature