The construction of supermatrices from mining of DNA metadata is problematic due to incomplete species identification and incongruence of gene trees that hamper sequence concatenation based on Linnaean binomials. We applied methods from graph theory to minimize ambiguity of concatenation globally over a large data set. An initial step establishes sequence clusters for each locus that broadly correspond to Linnaean species. These clusters frequently are not consistent with binomials and specimen identifiers, which greatly complicates...