Phylogenomic tree reconstruction at the FF level of structural classification. The SCOP database classifies protein domains into a hierarchy of fold families (FFs), fold superfamilies and folds. In this study, we counted multiple occurrences of individual FFs in proteomes to build data matrices. Matrices of genomic abundances are normalized in a scale of '0' to '9' and 'A' to 'N' and their columns and rows can be transposed to generate both trees of proteomes and trees of FFs.
Kim and Caetano-Anollés BMC Evolutionary Biology 2012 12:13 doi:10.1186/1471-2148-12-13