Table 1 Comparison of time series microarray software packages. The table presents a comparison of three microarray time series analysis software packages: STEM, GQL, and CAGED. The execution time results are based on running on the same dataset as in Figure 3. The default settings of STEM and CAGED were used. For GQL the initial collection of HMMs was set to six two state HMMs and six three state HMMs. The experiments were carried out on a Pentium 1 GHz with 512 MB of RAM.