Most of the trees computed from masked alignments using either NJ or ML methods were comparable to those computed from alignments without any missing data (mean stQD of 0.0022 and 0.0026 vs. 0.0 for full alignments).
Maximum likelihood phylogenetic analyses were performed as described above for the full alignment for each strategy of long-branch exclusion on each of three partition sizes of interest (full alignment, A136665, A133065, as discussed in Results).
PAGAN reconstructs graphs for all internal and extant nodes (totalling 10 999 for a full alignment) and needs 627 s and 2070 Mb for the analysis of the same data.
For the full alignment and Bayesian Ka/Ks ratios obtained from the models, see Figure S3.
For the full alignment of 237,882 16S rRNAs, the supports required just one hour.
We used the alignment shown in Figure 1 to construct a phylogeny of bacteriorhodopsins (see Additional file 1 for the full alignment).
Both RSS and CSS are mostly found in the conserved regions of RIFIN proteins (see Additional file 4, rifins_high.html, for the full alignment with stringent cut-offs).
The complex model of substitution including gamma distribution and invariant sites (GTR+Γ+I) was selected for the full alignment by the hierarchical likelihood ratio test (LRT) as well as the Akaike information criterion (AIC).
In Crenarchaeota, this tail appears to be involved in repair and recombination (Cubeddu and White 2005) (schematically represented by a striped box in fig. 5, for a full alignment see supplementary fig. S1, Supplementary Material online).
The function shift analysis of sub-group A against sub-group B (using standard cut-offs of 4 for RSS and 0.5 for CSS) resulted in the prediction of 81 rate shifting sites (RSS) (22% of all positions) and 60 conservation shifting sites (CSS) (17%) between them (see Additional file 3, rifins.html, for the full alignment).
