Maximum likelihood phylogenetic tree of human homeodomains excluding ANTP and PRD classes. Arbitrarily rooted phylogenetic tree of human homeodomains excluding the ANTP and PRD classes constructed using the maximum likelihood method. Bootstrap values supporting internal nodes with over 70% are shown. Homeodomain sequences derived from pseudogenes are excluded. Roman numeral suffixes are used to distinguish multiple homeodomains encoded by a single gene. Classes and/or families are color coded as shown in the key. The LIM and ZF classes are not recovered as two distinct monophyletic groups, a result also found by neighbor-joining analysis (Additional file 5). The multiple homeodomains of Zfhx-family proteins and Zhx/Homez-family proteins are also dispersed in the tree, presumably artefactually. Detailed relationships between different gene families should not be inferred from this tree.