When time is up, computed assemblies are sorted and the top ones are returned. The absolute upper bound is 12 hours. Note that no restriction is put on the first stage which may take very long in the cases with long genes. Each run can take a lot of computing resources. It is recommended to set these parameters small during first trials.
Computation can be very time-consuming especially in the cases when the target relative is distant.
Note that the Las Vegas algorithm requires at least 100 potential suboptimal exons in the second stage to make a decision. There are two different entry points of the software, the first one for amino acid sequence comparison and the second one for nucleotide sequence comparison. Note that specification of the appropriate target type is important for the amino acid version. When a user wants nucleotide sequence comparisons only, the use of the second entry point is recommended since it doesn't provide target type selection. The server keeps result files of a run for only 24 hours.