Results of the maximum parsimony analysis for Drosophila (DM) and mouse (MM) HOX genes and potential cnidarian HOX genes (Cnox). Numbers below branches are percentages (>50) of 100 bootstrap replicates. Numbers above are branch support estimates, the number of additional steps in the shortest cladogram lacking a particular node. The tree shown is a strict consensus of two most parsimonious cladograms (length: 2351 steps, consistency index: 0.453, retention index: 0.527) generated by a heuristic search with TBR branch swapping with 1000 random addition replicates. Sequence from both the hexapeptide and homeobox regions was used. Both amino acid and nucleotide sequence were included in the data set, with amino acid changes given three times the weight of nucleotide changes. Additional analyses were also performed using amino acid sequence alone, with changes weighted using the "protpars" matrix of PAUP 3.1.1, and using both amino acid and nucleotide data with equal weighting of amino acid and nucleotide changes. These analyses also supported a monophyletic group of medial genes that included no cnidarian representatives. Bootstrap replicates were performed using amino acid sequence alone, so that values would not be inflated by correlation between amino acid and nucleotide characters. Percentages of 100 replicates with SBR branch swapping are shown. Branch support values were calculated using the "constraints" option of PAUP 3.1.1, with TBR branch swapping on 200 random addition replicates.