The distance between each of the site stripped phylogenies and the ideal mammalian peroxidase phylogeny. (a) The ideal phylogeny pruned from the mammalian phylogeny by Murphy et al. (2001), the peroxidasin sequences are outgroups to the MHP clade. The following are the species abbreviations used: Dog (D); Cow (C); Macaque (Ma); Human (H); Chimp (Ch); Rat (R); Mouse (M), Chicken (G), and Opossum (Op). This phylogeny was compared to each of the resultant site stripped phylogenies. (b) Graph showing the RMSD nodal distance (y-axis) between each site-stripped phylogeny (x-axis) and the ideal phylogeny. On the X axis: All: refers to the complete MSA; 8: site category 8 removed from the MSA; 8, 7: categories 8 and 7 removed from the MSA and so on up to the final column that contains only the most slowly evolving category of site. Values close to/zero correspond to complete agreement between the ideal and site stripped phylogeny.
Loughran et al. BMC Evolutionary Biology 2008 8:101 doi:10.1186/1471-2148-8-101