Additional file 1.
Assignment of the Dlx probes to their group of orthologues. In order to assign each Dlx probe to an orthologous group, phylogenetic analyses were performed. The Dlx gene sequences of Triakis semifiasciata (leopard shark), Homo sapiens (human), Gallus gallus (chicken), Xenopus tropicalis (xenopus), Danio rerio (zebrafish) were retrieved from Ensembl release 49 and GenBank release 164. Multiple Dlx amino acid sequences were aligned using ClustalX (Thompson et al. 1997) with manual optimization using MUST software (Philippe 1993). Regions of ambiguous homology were removed. Evolutionary distances were computed using the Poisson correction and a neighbor-joining tree was obtained using MEGA4 (Tamura et al. 2007). The robustness of the tree nodes was estimated by a bootstrap test (1000 replicates). Philippe H. 1993. MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 21:5264-5272. Tamura K, Dudley J, Nei M, and Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882.
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Debiais-Thibaud et al. BMC Evolutionary Biology 2011 11:307 doi:10.1186/1471-2148-11-307