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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

Fig. 2

Flowchart of the consistency pipeline Given an inconsistent hierarchy of OGs, the consistency pipeline traverses the hierarchy of levels in reversed level order, i.e. starting from the leaves, every parent level is visited only after all lower levels have been visited (outer loop). To make each level hierarchically consistent with all its lower levels, the described six steps are applied for each inconsistency in the level (inner loop): (1) expansion of OGs between one parent level and its children levels, to identify hierarchical inconsistencies (red lines); (2) subsampling of the expanded OG (dashed oval) to obtain sequence samples; (3) Gene tree computation from the sequence samples and pruning of the general species tree to match individual gene tree samples; (4) reconciliation of gene tree and pruned species tree samples; (5) majority vote to determine the solution to resolve the inconsistency, i.e. merge or split; (6) propagation of the split decision if new inconsistencies arise in children’s descendant levels. The algorithm repeats until the root level is completed and the entire hierarchy will be consistent

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