Constructing benchmark test sets for biological sequence analysis using independent set algorithms
Fig 3
Each algorithm was run once on each Pfam seed and full alignment for at most 6 days. The runtimes are reported as a function of the product of the number of sequences and the number of columns in the alignment, as bar plots including outliers (translucent grey circles). The boxes extend from the first to third quartile, and the median is marked by a horizontal line. The results for families with at most 10,000 sequences were obtained on 2 cores and 8 GB of RAM, and the remaining were obtained on 3 cores and 12GB of RAM. The results do not include 34 families that Blue did not finish running within 6 days. Blue finished 939 of 944 families in the [106, 107) range, 58 of 85 families in the [107, 108) range, and 1 of 3 families in the [108, 109) range (and we omitted a bar plot for Blue for [108, 109)).