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Table 3 Running times on large data sets

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

 

# of sequences

 

20,000

40,000

78,132

weighted majority, 5 quartets

6m 41s

15m 52s

34m

FastTree (NJ phase only)

13m 52s

41m 15s

116m

  1. Running times of the random walk algorithm compared to FastTree. We used the huge.1 alignment from the original FastTree paper[9]. Smaller data sets were created by choosing a random subset of sequences from the large alignment. Our algorithm runs 2.1 to 3.4 times faster than FastTree on these very large data sets.