The tool requires that there be one or more complete, finished genome, and any number of draft sequences. It is based on suffix-tree algorithms (16) . It requires that anchors, identical sequence fragments of user-specified length, be found in each of the genomes to be aligned. Thus, there must be some level of sequence conservation among the genomes in order to discover anchors of sufficient length (e.g. 35-60 bp) that are present in all the genomes. Then the regions between the anchors are aligned using a tool, such as clustalw or HMMer. The algorithm functions most efficiently if anchors are frequent and dispersed across the genomes to provide even coverage. If substitutions, deletions, insertions or gaps in sequence information (e.g. between contigs) result in an anchor's absence in one or more of the genomes, then those regions must be aligned using clustalw, which is slower and more memory intensive for large amounts of sequence data. Similar to all anchor-based alignment algorithms, WGASA is dependent upon a high degree of co-linearity across all input genomes.