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Table 1 AAF performance metrics

From: An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

Coverage Filtered Memory (MB) Generating k-mer table (CPU hours, using one core) Calculating distance matrix (CPU hours, using one core)
5X no 68,082 117 103
5X yes 68,086 85 56
2X no 39,780 66 61
2X yes 39,048 39 22
1X no 34,316 50 8
  1. Performance metrics for the AAF reconstruction of the 11-primate phylogeny from simulated SRS data using one thread only. Phylogenetic reconstruction requires generating the k-mer table and calculating the number of shared k-mers between species to compute the distance matrix. Note that the memory usage is for the first step; the second step required no more than 1G of memory