The exponential accumulation of genomic sequence data demands systematic analysis of genetic information and requires use of various computational approaches to handle such huge sets of genomic data. Comparative genomics, with such organized data and diverse computational techniques, has become useful not only for finding common features in different genomes, but also for understanding evolutionary process and mechanism among multiple genomes.

Comparison of multiple genomes is a challenging task partially because combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool and partially because it handles a huge amount of data. Another problem is the subjectivity of how to select multiple genomes. For example, there are 1,313,400 (= 200 3) possible selections of three genomes out of 200 completely sequenced genomes. The inconsistency of input data from existing sources and the effective presentation of analysis result also raise problems.

Considering all these issues, it is not possible to perform multiple genome comparison on the web by simply using sequence analysis tools in an ad hoc fashion.