A limitation of all inferred phylogenetic data is that it is directly dependent on the alignment and less so on the programs used to build the phylogenetic tree [39] . One of the shortcomings of automated alignments may thus derive from the fact that they commonly employ a scoring and penalty procedure to find the best possible alignment, since these parameters vary from species to species [22, 23] , as mentioned above. Careful inspection of alignments is therefore advisable, even though software has been developed that combines the alignment procedure and phylogenetic analysis iteratively in one single program [40] .