2.2 Input and Output files
PAReTT uses two primary forms of input that are specified when the user is prompted to provide the name of the input file. The first is a basic text file, indicated as “.txt”, while the second is a standard comma separated value file, indicated as “.csv”. While it is preferred to specify the full name of the file (e.g., “Species.txt”), PAReTT was scripted with checkpoints to ensure the proper format of input files even when only a name is given and should read the input file as long as they are in the current working directory. If the files are not stored in the current working directory the full file path is preferred.
Output files differ based on the specific data being retrieved. For example, timelines are retrieved as pictures in the JPEG format while time trees for both taxa as well as specific lists of species are retrieved in the Newick format, which is readable by most phylogenetic software programs including FigTree (Rambaut, 2017) and MEGA (Kumar et al. , 2018); these trees can also be viewed directly in PAReTT. Any species in the provided list for which the divergence time could not be resolved in the tree or were substituted by a similar species are stored as a table for review. Divergence time data for pairs are printed on screen and divergence times, based on the mean adjusted time, for species lists are stored in ‘dataframe’ objects and provide the option to store the output as a vectorized three column matrix in a comma separated value file. Output files are stored in the active working directory.