There has been considerable discussion recently regarding how to align large sets of DNA sequence data that contain regions of ambiguity. We examine and discuss several genome-scale alignment methods, including “fragment level” and “elision” (concatenation), focusing on sequence data from the chloroplast inverted repeat from currently published genomes. We also include homologous sequences from taxa that no longer have the inverted repeat or have a highly reduced repeat. Sequences are from several green algal groups, liverwort, fern, gymnosperm and angiosperms. We also present an update on the status of sequencing complete fern chloroplast genomes. Comparisons of several vascular plant genome sequences are then presented. We show the utility of the data for inferring deep phylogeny and for examining genome evolution.

Key words: alignment, chloroplast genome, genome evolution, plastid genome