Figure 4

Maximum likelihood phylogenetic tree of the pol region of Copia elements from the genome of Anopheles gambiae. The final alignment encompasses a region of 1928 aa positions. The tree was generated using default settings for MUSCLE 3.7 (as alignment tool), Gblocks 0.91 b for alignment refinement, PhyML for tree generation, and TreeDyn for tree drawing as implemented in [69]. Red numbers above the branches indicate a confidence index based on the approximate likelihood-ratio test (aLRT) for branches [72]. An * indicates sequences identified in AnoTExcel. Three sequences belonging to the Pao-Bel superfamily were used as outliers for tree construction.