Proportion of perfectly phased SNP pairs and vector error rate for RL (solid line) and MEC (dashed line) optimization in 10000 trials over 5×, 10×, 20× and 100× coverage.

<p>Proportion of perfectly phased SNP pairs and vector error rate for RL (solid line) and MEC (dashed line) optimization in 10000 trials over 5×, 10×, 20× and 100× coverage.</p

Loss of function in different polyplotypes of a sample pentaploid genome.

<p>As the loss of function is often determined by whether a healthy copy of a gene exists, knowing the genotype vector is sufficient if there is a single SNP site. In the case of two SNP sites however, the genotype vector cannot be used to unambiguously determine loss of function, and phasing is required.</p

HapTree (solid lines) and HapCompass (dashed lines) on simulated triploid genomes: Likelihood of Perfect Solution and Vector Error Rates, 1000 Trials, Block lengths: 10, 20, and 40.

<p>HapTree (solid lines) and HapCompass (dashed lines) on simulated triploid genomes: Likelihood of Perfect Solution and Vector Error Rates, 1000 Trials, Block lengths: 10, 20, and 40.</p

Examples of <i>Vector Error</i> in a sample tetraploid genome; the true phase is on the left and examples with two, three, and four vector errors are on the right.

<p>Examples of <i>Vector Error</i> in a sample tetraploid genome; the true phase is on the left and examples with two, three, and four vector errors are on the right.</p

HapTree (solid line) and HapCompass (dashed line) on simulated tetraploid genomes: Likelihood of Perfect Solution and Vector Error Rates, 1000 Trials, Block length: 10.

<p>HapTree (solid line) and HapCompass (dashed line) on simulated tetraploid genomes: Likelihood of Perfect Solution and Vector Error Rates, 1000 Trials, Block length: 10.</p

Results of switch error (switch) and MEC score for HapTree and HapCUT of whole-genome phasing using 454 and Illumina data.

<p>Results of switch error (switch) and MEC score for HapTree and HapCUT of whole-genome phasing using 454 and Illumina data.</p

HapTree performance over varied error rates (.001, .02, .05, .1) and coverages (10×, 20×, 40×) on simulated triploid genomes: Likelihood of Perfect Solution and Vector Error Rates, 10000 Trials, Block length: 10.

<p>HapTree performance over varied error rates (.001, .02, .05, .1) and coverages (10×, 20×, 40×) on simulated triploid genomes: Likelihood of Perfect Solution and Vector Error Rates, 10000 Trials, Block length: 10.</p