Additional file 2.

Neighbor-joining phylogenetic tree of all human plus selected protostome and cnidarian homeodomains for identification of gene families. Arbitrarily rooted phylogenetic tree of all human plus selected protostome and cnidarian homeodomains constructed using the neighbor-joining (NJ) method. Bootstrap values supporting gene family designations are shown. Homeodomain sequences derived from pseudogenes are excluded. Comparison of NJ and ML trees, and description of the dataset used, is given in the legend to Additional file 1. Several artefactual mixing of classes occurs in this NJ tree, notably splitting of the CUT class, mixing of the TALE and SINE classes and aberrant placement of HOPX.

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Holland et al. BMC Biology 2007 5:47   doi:10.1186/1741-7007-5-47