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. 2005 Apr 19;6:102. doi: 10.1186/1471-2105-6-102

Figure 4.

Figure 4

Effects of parameter changes on alignment accuracy and relative error in evolutionary distance estimation. Ordinate axes are scaled to match Figure 3. Alignment accuracy (A, C, E, G, &I) and evolutionary distance estimation (B, D, F, H, &J). (A &B) Effect of initial sequence length. (C &D) Effect of mean insertion and deletion size. (E &F) Effect of insertion and deletion rate. (G &H) Effect of intersite rate variation. (I &J). Effect of nucleotide frequency bias (G+C content). Error bars represent ± one standard deviation. Black and white points represent HKY simulations with expected distances of 0.5 and 1.0, respectively.