. 2016 Mar 1;32(3):262–270. doi: 10.1089/aid.2015.0189

Table 2.

Summary of Tests of Compartmentalization Comprising Tree-Based (^*) and Diversity-Based (#) Algorithms

	Intracompartment diversity^#^,a							CCR5 usage^f,g
Patient number	Plasma (± SD)	Tissue (± SD)	p-value (z-test; t-test)	SM^,b*	R^*^,c	r-b^*^,d	Hudson^#^,eS-nn	Plasma (no. and % clones)	Tissue (no. and % clones)
TB12	0.008 ± 0.001	0.006 ± 0.001	0.29; 0.30	4 × 10⁻⁵	0.002	0.002	0.262	9 (100)	9 (100)
TB25	0.002 ± 0.001	0.017 ± 0.002	9.9 × 10⁻⁷; 1.02 × 10⁻⁶	6.7 × 10⁻⁵	0.002	0.002	0.000	8 (100)	8 (100)
TB32	0.002 ± 0.0002	0.040 ± 0.012	0.46; 0.46	0.022	0.002	0.03	0.000	9 (100)	4 (100)
TB16	0.002 ± 0.0002	0.008 ± 0.001	0.02; 0.02	0.0005	0.002	0.002	0.000	6 (100)	9 (100)
TB20	0.058 ± 0.003	0.002 ± 0.001	0.00; 0.29	0.0003	0.002	0.002	0.000	6 (77)	9 (100)
TB38	0.052 ± 0.008	0.005 ± 0.001	0.006; 0.09	0.001	0.004	0.002	0.000	6 (100)	7 (100)

^{^a}

Intracompartment pairwise distance (DIVEIN).

^{^b}

Slatkin–Maddison test (HyPhy).

^{^c}

Branch length correlation coefficient (r, HyPhy).

^{^d}

Branch count correlation coefficient (rb; HyPhy).

^{^e}

Hudson nearest neighbor (Snn; HyPhy).

^{^f}

Coreceptor usage is indicated as percentage number of sequences.

^{^g}

Coreceptor usage potential was analyzed using the online tool Geno2Pheno (www.geno2pheno.org) that uses sequence data and support vector machine (SVM) classifiers to predict coreceptor usage.

Tests of compartmentalization were executed in DIVEIN and HyPhy software packages indicating statistical support for divergence and anatomical compartmentalization.

Statistical significance is indicated by p values where values <0.05 are underlined and <0.005 appear in bold.