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Figure 5 | BMC Bioinformatics

Figure 5

From: Logarithmic gap costs decrease alignment accuracy

Figure 5

Accuracies of best costs plotted by divergence. I, I A , and I L are the alignment identities produced by the best log-affine, affine, and logarithmic gap penalties, respectively. See Figure 3 for more information. a-c) Alignment identities plotted by the branch length of the alignments. Divergence time is plotted on a uniform scale, u = 1 - exp (-t/ t ¯ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWG0baDgaqeaaaa@2E35@ ). d-f) Box-whisker plots of identities grouped into 20 bins of 250 values. Solid bars are medians. Notches are significant range of medians. Bars are the mid-range. Whiskers are the range. Circles are outliers.

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