Maybe further clarification will help. I have a software used for bioinformatics that reconstructs interaction networks, think genes for example. Briefly, points (or experiments) are randomly sampled from the original data set with replacement and assembled into new 'bootstrapped' data sets containing the same number of experiments as the original. The software is then applied to a large number of such pseudo-data sets to generate a set of bootstrap networks. A consensus network is then constructed that includes edges (i.e., interactions) that are supported across many of the bootstrap networks. The first script, 'qsubbootstrap.pl', is used for the submission of bootstrap jobs to computational clusters. The first argument to this script is the name of the output directory, and the second and third arguments specify the range that is used to number the resulting files. Upon completion of the jobs, executing the second script, 'getconsensusnet.pl', will combine all the adjacency matrices and randomly permute the inferred edges in each bootstrap network to perform significance tests. It will then construct the consensus network based on the user-specified P-value threshold. This script takes as arguments the directory containing the bootstrap networks and the significance threshold. For example, 'perl Scripts/getconsensusnet.pl BoostrapNetworks 1e-7' will construct a consensus network from all bootstrap networks contained in the 'BootstrapNetworks' directory using significance threshold '1e-7'. I want to employ a similar procedure in a related program that calculates two sets of mutual information as described in my first post. Will such an implementation be possible?