Overview of ASAP Data Flow. Data originate in the form of either a collection of systematically annotated FASTA files (1), a NEXUS file with partitions delineated using the CharPars command (2), or a list of NCBI GI/Accession numbers that are organized according to partitions (3). An alignment tool, such as MUSCLE, is applied to unaligned data (A). At this stage, ASAP will assemble a NEXUS file that is a compilation of all the data partitions and performs a tree search to generate a simultaneous analysis tree (4) as well as the requisite tests to determine the hidden branch supports on this tree (5). The results of the hidden branch supports are saved to a tab-delimited text file that can be imported into popular spreadsheet applications like Microsoft Excel.