Consistent neisserial phylogenetic trees. (a) From the concatenated ubiquitous gene alignment (numbers indicate nonparametric bootstrap results in percentage out of 1,000 experiments); (b) from the concatenated 1,000 nucleotides regions (± 500 nucleotides) surrounding ubiquitous DNA uptake sequence (DUS) sites in the M-GCAT multiple alignment; and (c) entire concatenated M-GCAT multiple alignment. Distance matrices were computed from the alignments using Tree-Puzzle  by maximum likelihood with the HKY+Γ model and trees computed with BIONJ .
Treangen et al. Genome Biology 2008 9:R60 doi:10.1186/gb-2008-9-3-r60