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Table 1 Comparison of the alignment-free distances and the MSA distance for NGS short reads of the mtDNA sequences

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

  d NCD d d CDM CVTree (k=10) d 2 S (k=8)
454 14 16 10 10 6
Exact 8 8 8 8 8
Empirical 6 8 4 8 12
Sanger 10 14 8 14 8
454 0.68 0.66 0.68 0.75 0.88
Exact 0.69 0.68 0.68 0.71 0.88
Empirical 0.69 0.69 0.66 0.69 0.81
Sanger 0.67 0.67 0.65 0.74 0.87
  1. The short reads were simulated from the mtDNA sequences using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5 × sampling depth. The two smallest tree symmetric differences and the two highest distance correlation coefficients for each error model are highlighted in boldface. Similar results for 1 ×, 10 ×, and 30 × sampling depths can be found in Additional file 1: Table S2.