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Figure 2 | Algorithms for Molecular Biology

Figure 2

From: Towards a practical O(n logn) phylogeny algorithm

Figure 2

Comparison of the random walk algorithm and FastTree. The performance of the random walk algorithm and FastTree as a function of the length of the sequences. The four graphs represent the performance on 10 tree topologies with branch lengths scaled by constant factors 25,50,100, and 200. In all cases, the random walk algorithm compares increasingly favourably with FastTree as the sequence length increases. After applying local search, the differences between the average accuracies of the two methods are less than 1% for all the settings except the shortest sequences in the data set scaled by 200, where trees obtained from FastTree are 3.8% more accurate. The average taxon coverage for random walk trees was 97.3%, with only three experimental settings yielding coverage below 95%. Missing taxa were inserted into random walk trees before applying local search.

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