Two different strategies of site removal to reduce systematic error. Because the G+C content is heterogeneous across species, taxa E and F are erroneously recovered as a sister-group of taxon J in the phylogeny based on a phylogenomic dataset due to convergently acquired high G+C content. The standard approach consisting of removing the fastest evolving sites does not alleviate this artefact. The second strategy proposed by Husník et al.  consists of removing the positions that contain both A/T and G/C nucleotides, and thus are more likely to be compositionally biased. The method is more effective in recovering the correct topology (right side of the figure) when compositional bias is the main cause of systematic error.
Philippe and Roure BMC Biology 2011 9:91 doi:10.1186/1741-7007-9-91