Additional file 1.

Amino acid alignment of all nematode taxa used for phylogenetic analysis. Alignment output from Gblocks. The Gblocks server http://molevol.cmima.csic.es/castresana/Gblocks_server.html webcite was used to align the concatenated amino acids using the most conserved settings. Blocks of "XXXX" represent markers between genes and were not included in the analyses; parameters are listed at the end of the alignment. Gblocks selected 2837 positions (marked *) to be included. Gene partitions are in the following order: atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4L, nad5, nad6. The concatenated mt genomic sequences used in the alignment represent species of Mermithida (Agamermis sp., Thaumamermis cosgrovei and Strelkovimermis spiculatus), Ascardida (Anisakis simplex, Ascaris suum and Toxocara canis), Dorylaimida (Xiphenema americanum), Rhabditida (Caenorhabditis elegans, Steinernema carpocapsae and Strongyloides stercoralis), Spirurida (Brugia malayi, D. immitis and O. volvulus) and Strongylida (Ancylostoma caninum, Ancylostoma duodenale, Bunostomum phlebotomum, Cooperia oncophora, Haemonchus contortus and Necator americanus). The species used as outgroups are denoted in bold text.

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Jex et al. BMC Genomics 2009 10:79   doi:10.1186/1471-2164-10-79