Additional file 8.
Examples of phylogenetic trees (Neighbor-joining) obtained for gene families having a putative pseudogene in Xff 4834-R: (a) XFF4834R_chr05500 is a frameshifted gene for which two overlapping peptides could be predicted and phylogenetic tree has a topology similar to that of housekeeping genes, (b) XFF4834R_25070-25100 is disrupted by ISXax1insertion (c) XFF4834R_chr25180 is a degenerated fragment of pigH, probably related to an integron insertion acquired from Xcc and (d) XFF4834R_chr33800 is a frameshifted gene for which two peptides could still be predicted.
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Darrasse et al. BMC Genomics 2013 14:761 doi:10.1186/1471-2164-14-761