Sequence Alignment, Parameter Sensitivity, and the Phylogenetic Analysis of Molecular Data

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Abstract
The dependence of the results of molecular phylogenetic sequence analysis (both alignment and cladogram construction) on variation in analytical parameters is examined. Phylogenetic analyses of molecular sequence data are necessarily based on intrinsically immeasurable parameters such as transition–transversion and alignment gap cost ratios (among others). Procedures for robust and liberal hypothesis choice are proposed using congruence as an optimality criterion. To illustrate and explain this process further, data on arthropod relationships are used. The effects of variation in transversion–transition and gap–change ratio parameters on alignment and phylogeny reconstruction are assessed in light of both taxonomic and character-based congruence measures.

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