1. A Coalescence-Guided Hierarchical Bayesian Method for Haplotype Inference 
Yu Zhang, Tianhua Niu, Jun S. Liu 
The American Journal of Human Genetics 
Volume 79, Issue 2, Pages (August 2006)
DOI: /506276
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

2. Figure 1
Schematic diagram of CHB. Hyperparameter ϴ* represents the frequencies of ancestral haplotypes from which the current samples are descended. Assuming a robust star-like topology, we derive the prior expectation of the modern-day haplotype frequencies, ϴ, as f(ϴ*), which takes into consideration both mutation and recombination events. Each haplotype consists of four SNPs, with 0 and 1 indicating the two alternative alleles.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

3. Figure 2
Mean error rates of CHB-NR (triangles), PHASE-NR (squares), and HAPLOTYPER (diamonds), for coalescence-based simulation data sets with no missing genotypes (left panel) or 30% missing genotypes (right panel).
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

4. Figure 3
Mean error rates and SEs of CHB-NR (white), PHASE-NR (black), and HAPLOTYPER (gray), for Whitehead IBD data sets with no missing genotypes (left panel) or 30% missing genotypes (right panel).
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

5. Figure 4
Mean error rates and SEs of CHB-NR (white), PHASE-NR (black), and HAPLOTYPER (gray), for HapMap data sets without recombination and with no missing genotypes (left panels) or 30% missing genotypes (right panels). Upper panels, European ancestry. Lower panels, African ancestry.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

6. Figure 5
Mean error rates and SEs of CHB-NR (white), CHB-R (light gray), PHASE-NR (black), and PHASE-R (dark gray), for HapMap data sets with recombination hotspots and with no missing genotypes (left panels) or 30% missing genotypes (right panels). Upper panels, European ancestry. Lower panels, African ancestry.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

7. Figure 6
CHB recombination estimation (upper panel) compared with the HapMap report of recombination rates for 1,081 SNPs across a 3-Mb region (lower panel). The upper panel displays the estimated average recombination probabilities across four populations from the HapMap project. Only values >0.1, which correspond to the highest 10% of recombination probabilities, are shown.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

8. Figure B1
Difference of phasing accuracy by running PHASE with 10 times number of iterations. M = mutation-only data; M+R = data in which both mutation and recombination are involved; +30% = data sets with 30% missing genotypes. Upper panel, HapMap data sets with European ancestry. Lower panel, HapMap data sets with African ancestry.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

9. Figure B2
Comparison between CHB-NR (triangles) and PHASE-NR (squares) on coalescence-based simulated data set (a), Whitehead IBD data set (b), and two HapMap data sets with no recombination: CEU (c) and YRI (d). In addition, the comparison between CHB-R (triangles) and PHASE-R (squares) of data sets with recombination hotspots is shown for CEU (e) and YRI (f). From each data set, 10% of genotypes were randomly removed.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

10. Figure B3
Comparison among CHB-NR (white), PHASE-NR (black), and HAPLOTYPER (gray) on TAP2 data sets with no missing genotypes (left panel) or 30% missing genotypes (right panel).
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

11. Figure B4
Comparison between CHB-NR (triangles), PHASE-NR (squares) and HAPLOTYPER (diamonds) on HapMap data sets with no recombinations from different populations: a, Han Chinese population with no missing genotypes; b, Japanese population with no missing genotypes; c, Han Chinese population with 10% missing genotypes; d, Japanese population with 10% missing genotypes; e, Han Chinese population with 30% missing genotypes; f, Japanese population with 30% missing genotypes.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

12. Figure B5
Comparison between CHB-NR (white), CHB-R (light gray), PHASE-NR (black) and PHASE-R (dark gray) on HapMap data sets with recombination hotspots from different populations: a, Han Chinese population with no missing genotypes; b, Japanese population with no missing genotypes; c, Han Chinese population with 10% missing genotypes; d, Japanese population with 10% missing genotypes; e, Han Chinese population with 30% missing genotypes; f, Japanese population with 30% missing genotypes.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions

13. Figure B6
Comparison between CHB-NR (white), CHB-R (light gray), PHASE-NR (black), and PHASE-R (dark gray) on HapMap data sets with moderate recombinations from different populations: a, European population with no missing genotypes; b, African population with no missing genotypes; c, European population with 10% missing genotypes; d, African population with 10% missing genotypes; e, European population with 30% missing genotypes; f, African population with 30% missing genotypes.
The American Journal of Human Genetics  , DOI: ( /506276)
Copyright © 2006 The American Society of Human Genetics Terms and Conditions