The running time of IAMBEE is determined by:
- The size of the network used as prior scaffold
- The setting of the running parameters (see parameters)
- The number of mutations and/or conditions in the input file.
We would suggest the user to start with a network of about 15000 edges. In the mutation file, either include only the most relevant mutations (the ones with a high frequency in the population, on the non synonymous mutations etc) or use all mutations but then provide additional info on their functional impact score or frequency increase during the selective sweep to allow IAMBEE to make a soft selection (by weighting the paths based on the relevance scores of the mutations).