Solution of the enolase phylogenic incongruence. (A) Multiple alignment based (MAB) tree. (B) TULIP tree. Both trees were constructed using the BLOSUM 62 similarity matrix. For MAB tree construction, bootstrap support was estimated using 1000 replicates. To build TULIP trees, Z-scores were estimated with 2000 sequence shuffling. Clades that contain a unique insertional signature (Land plants, green box; Charophytes and Chlorarachnion, blue box; Alveolates; yellow box) are not gathered in the MAB tree, as previously reported . By contrast, in the TULIP tree, the phylogeny of enolase proteins is reconciled with the insertional signature detection in Land plants, Charophytes, Chlorarachnion and Alveolates.