Dataset | Phylip | Naive | Fastdist | NJ |
|---|
Birds [10] | 119 m40 s | 257.4 s | 35.12 s | 20.4 s |
Hepatitis C [9] | 23 m | 25.9 s | 6.37 s | 0.35 s |
- Comparing the running time of Phylip's dnadist, our optimized implementation of the naive approach, and the new algorithm fastdist (without the resolution technique) on real world biological datasets when 1000 bootstrap evaluations were performed. The NJ column describes the time it takes to reconstruct the 1000 trees using the implementation of [2]. The dataset Birds [10] contains 146 copies of a nuclear gene in birds with a sequence length of 2974. The dataset Hepatitis C [9] contains 29 RNA sequences of length 9168 from the Hepatitis C Virus. Using the wc unix utility for reading the file containing 1000 bootstrapped datasets of [10] takes 4.35 seconds and reading the datasets of [9] takes 2.66 seconds.
