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Figure 5 | BMC Evolutionary Biology

Figure 5

From: Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes

Figure 5

Examination on the effect of HPAA tracts in lamprey Emx sequences. (a) Schematics of lamprey Emx sequences used in this analysis. The A-tract (A) and Q-tract (Q) correspond to those indicated with gray background in Figure 2. The two intact or artificially modified (ΔHPAA) lamprey Emx sequences were aligned with their homologs by using ClustalW, MAFFT, or T-Coffee. The resultant multiple alignments were passed on to selection of amino acid sites using TrimAl with different settings (see Methods). (b) Comparison of degrees of the support for the lamprey EmxA-EmxB grouping. RELL bootstrap probabilities for this relationship were computed in a ML analysis by inputting datasets prepared with the variable stringencies in site trimming with TrimAl (no gap allowed and st of 0.00001 to 0.001), as well as variable choices of alignment programs and the presence or absence of the HPAA tracts (see Methods).

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