Stability in phylogenetic formulations and its relationship to nodal support.

The phylogenetic analysis of nucleic acid sequences, as with other data, is unavoidably based on explicit and implicit assumptions. At the fore are character transformation models—usually transversion– transition ratios–and the relative cost of alignment-derived sequence gaps. These values are the fulcra of sequence analysis. Simple homogeneous weighting does not avoid the issue of arbitrary, yet crucial, assumptions. (Wheeler, 1995:321) Sensitivity Analysis (SA) is the study of how variation in the output of a model can be apportioned, qualitatively or quantitatively, to different sources of variation, and how the given model depends upon the information fed into it. (Saltelli, 2000:3)