Figure 2
From: Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score
The DomRefine pipeline. The pipeline is given a domain-level ortholog clustering result and modifies domain organizations using five procedures. Domain organizations are illustrated using light blue and pink colors. Multiple alignments of amino acid sequences are represented by sets of aligned horizontal lines. Adjacent clusters are merged if the score increases by merging the clusters (merge). Given a pair of adjacent clusters, adjacent domains are temporarily merged and then divided into clusters considering score changes on the phylogenetic tree (merge_divide_tree). Existing boundaries are moved (move_boundary), and new boundaries are created (create_boundary). When species overlap between sub-clusters on the phylogenetic tree is detected, the cluster is divided into subgroups (divide_tree).