Figure 1.

Flow chart of SwiftOrtho. SwiftOrtho is a graph-based method that consists of 3 major steps. (i) All-vs-all homology search: a seed-and-extension method is used to perform a homology search. (ii) Orthology inference: nodes are gene names; edges are similarity score of pairwise genes. 1. A₁-B₁ are putative orthologs identified by RBH; 2. A₁-A₂ and B₁-B₂ are putative in-paralogs because the bit scores of these pairs are greater than A₁-B₁; 3. A₂-B₁ and A₂-B₂ are putative co-orthologs because these pairs are not orthologs but A₁-B₁ are orthologs and A₁-A₂, B₁-B₂ are in-paralogs. (iii) Cluster analysis: Markov clustering or affinity propagation algorithm is used to cluster orthology relationships.