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

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

	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

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.

ISSN: 1756-0500