AliGROOVE example results of 4-taxon simulation tests (simulation setup A). AliGROOVE similarity scores and identified branch reliability of best Maximum Likelihood (ML) topologies obtained for different branch elongations of two non-directly related terminal branches (L1, L2) (Figure 1a) considering nucleotide and amino acid data (sequence length: 250,000 bp). The two graphs below show the reconstruction success in relation to the length of long branches (BL2). Note that amino acid sequences are more reliable. Colour coded similarity score ranges are shown in the center. Lacking reliability of internal branches (red internal branch) is observed for incorrect ML topologies predominating in 100 data replicates conducted for each length of BL2. Boxes with coloured squares show scores for pairwise sequence comparisons. In the corresponding topologies unreliable branches are shown in red. Circles indicate whether the topologies are correct (blue) or wrong (red). All results of 4-taxon simulations are given as Additional files 1 and 2.