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Fig. 2 | BMC Evolutionary Biology

Fig. 2

From: MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

Fig. 2

Performance comparison in terms of runtimes and MP scores between MPBoot SPR6 and intensive-TNT under uniform (a, b) and non-uniform cost matrices (c, d), for real DNA and amino-acid MSAs. Each dot in the main diagrams represents a single MSA. The y-axis displays the difference between the CPU times of the two programs. The x-axis displays the difference between parsimony scores of the MP trees on the original MSA inferred by the two programs. The histograms at the top and the side present the marginal frequencies. Dots to the left of the vertical dashed line represent alignments where MPBoot found a better parsimony score. If a dot is below the horizontal dashed line, the bootstrap analysis by MPBoot was faster. Percentages in the quadrants of histograms denote the fraction of alignments in that region. Percentages on the dashed line reflect the number of alignments where two programs obtain equal MP scores

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