Effect of excluding gaps and variable regions. The plot shows the effect of filtering on the minimum duplication test with back-translated, fungal amino-acid alignments. Removing gapped sites tends to worsen the accuracy of the induced maximum likelihood trees. Removing variable regions in addition to gapped sites (Gblocks, default settings) drastically reduces the accuracy of reconstructed trees. Error bars correspond to ± 1 s.d. Significant difference between results from original and curated alignments is denoted with a minus symbol at the basis of relevant bars (Wilcoxon double-sided test, P < 0.01).
Dessimoz and Gil Genome Biology 2010 11:R37 doi:10.1186/gb-2010-11-4-r37