Figure 2

A flowchart of the algorithm for a given gene segment. MuLDAS starts by aligning the query with the pre-maid MSA of reference sequences, which includes CRFs in HIV-1. Through this, the gene segments to which the query maps are identified and the whole process is repeated over these gene segments. After distance matrix is obtained, MDS and LDA are performed to classify the query. In HIV-1, only the major groups are used in this step. The genotype gives rise to the best posterior probability is reported as the major genotype. If nested analysis is not required as for HCV, the process stops here. Otherwise as for HIV-1, an additional process called nested analysis (shown in red) is performed. For the major analysis, the genotypes that give rise to P > 0.01 and their associated CRFs are identified, and the subset of the distance matrix corresponding to these genotypes is excised from the original matrix saved in the major analysis. After MDS and LDA, the best genotype is reported as the nested genotype. Once both nested and major genotypes are determined, a decision process outlined at the bottom proceeds from left to right and suggests the final outcome (see "a proposed process for subtype decision" section for details).