Fig. 4

Graphical illustration of the MLCA algorithm. The evolutionary hypothesis for a virus within a GLUE project consists of an alignment of reference sequences R₁,…,R₇, a reference phylogeny with these sequences as leaf nodes and a set of clade definitions. In its initial alignment step, MLCA extends the reference alignment with a row for query sequence Q. Next, the placement step (RAxML EPA) suggests a branch for Q within the reference phylogeny. Finally, the Neighbour-weighting step assigns clades to Q by analysing the location of the additional branch in relation to neighbouring reference sequence taxa