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Table 5 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+local search

20m 40s (27m 21s)

41m 33s (57m 25s)

79m (113m)

FastTree + local search

21m 27s (35m 19s)

42m 29s (83m 44s)

80m (196m)

  1. Running times of the local search procedure of FastTree applied to trees produced by our algorithm and the Neighbour Joining phase of FastTree on the huge.1 data set. Total runtimes, including the time required to produce the initial tree, are shown in brackets.
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Algorithms for Molecular Biology

ISSN: 1748-7188