Skip to main content

Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29 Escherichia/Shigella genomes

From: Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction

  d NCD d d CDM CVTree(k= 9) CVTree(k= 15) CVTree(k= 21) d 2 S (k=8)
454 16 14 12 22 22 54 50
Exact 12 10 10 22 24 36 50
Empirical 16 12 14 24 18 42 54
Sanger 12 10 10 28 24 40 50
454 0.96 0.96 0.97 0.74 0.87 0.31 0.04
Exact 0.97 0.97 0.98 0.82 0.82 0.61 0.05
Empirical 0.96 0.96 0.96 0.77 0.85 0.38 0.01
Sanger 0.97 0.97 0.97 0.78 0.86 0.36 0.04
  1. The short reads were simulated from the Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1 × sampling depth. The two smallest tree symmetric differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5 × sampling depth can be found in Additional file 1: Table S3.