Figure 3.

Prune partitioning of a phylogenetic tree of 44 species. Prune run with a maximum sub-tree size of 10 sequences breaks the tree into seven sub-trees. Six of the sub-trees (light gray) can be aligned in parallel because they contain only known leaf sequences (filled squares; out-groups for sub-trees are not shown). Once these six sub-trees are aligned and the sequence of the roots (filled circles) is inferred, the internal sub-tree (dark gray) can be aligned. Note that this sub-tree includes both leaf sequences and inferred sequences. The alignments from the light gray sub-trees are merged with the alignment of the dark gray sub-tree to form the alignment of the entire tree.