854745.fig.006
Figure 6: Phylogenetic analysis of XPA proteins. A representative ME tree with branch lengths in units of number of amino acid substitutions per site is shown. Bootstrap values for 1000 replicates for MP/ML/ME trees shown next to branch points. Positions containing gaps and missing data were eliminated. MP tree was obtained using the close-neighbour-interchange method with initial trees obtained by random addition of sequences. Initial tree for ML was constructed using BioNJ method with nearest neighbour interchange used for tree topology search. Discrete gamma distribution with 4 categories was used to model evolutionary rate differences among sites. For ME tree, evolutionary distances were computed using p-distance method and tree was searched using close-neighbour-interchange algorithm.