Input

MultiPhATE2 is invoked using a single input parameter consisting of a configuration file, as follows: $python multiPhate.py multiphate.config. The configuration file allows the user to specify (a) genomes to be processed, (b) gene finder(s) to be used, (c) PhATE annotation search algorithms and databases, (d) blast cutoffs, (e) locations of databases, (f) Compare Gene Profiles matching cutoff, (g) PhATE, Compare Gene Profiles, and Blast+ multiprocessing, (h) stopping points, (i) checkpoints, and (j) console messaging verbosity. Concise instructions for creating a multiphate configuration file are provided in the project README, the project wiki, and in the sample.multiphate.config file itself, provided with the multiPhATE2 distribution. Code execution can be tailored to run specific gene finders and to search for homologous sequences in specific phage- and virus-centric data sets, in addition to more generic protein data sets.