Efficient implied alignment

摘要

Implied Alignment (IA) was proposed by [1] as an adjunct to Direct Optimization (DO) [2, 3] to be used in phylogenetic tree search to provide both verification and more rapid heuristic analysis. The method was originally implemented in later versions of MALIGN [4] and has been a component of POY [5–9] since its inception. A more formal description of the algorithm was presented in [6] and [2]. Although originally designed for alignment-free phylogenetic analysis (dynamic homology, [10]), the procedure was first used as a stand-alone multiple sequence alignment (MSA) tool by [11] in their analysis of skink systematics.