UNIX When Hy-Phy starts up, its default behavior is to scan for and display the list of currently available standard analyses. You can select a standard analysis to run by typing in its abbreviation (specified in the list). Hy-Phy will not display the list of standard analysis in 2 cases: 1. A batch file to process was passed to Hy-Phy via a command line argument 2. Hy-Phy could not locate the TemplateBatchFiles directory. If TemplateBatchFiles is not in the current working directory, you may need to explicitly tell Hy-Phy where the standard analyses are located. To do so, use the BASEPATH=absolute path to Hy-Phy installation directory (no spaces and all capital letters in BASEPATH) command line argument. For example, if you running Hy-Phy from the directory /home/joeuser/, and the Hy-Phy installation is located in /usr/local/HYPHY/, then you would execute (assuming that /usr/local/HYPHY/ is in the search paths), HYPHYKernel BASEPATH=/usr/local/HYPHY/ In most cases, there should be a system wide alias which will automatically include the BASEPATH argument. All standard analyses include prompts from data files and similar input. A typical prompt will look like this: Select a nucleotide file(/home/joeuser/): The path in parentheses is the current base for Hy-Phy relative path names. For instance, if you supply data/50seq.nuc as the input to the prompt, Hy-Phy will look for the file /home/joeuser/data/50seq.nuc. You can specify an absolute path name as input to any file related prompts, and use ../ in relative paths to refer to parent directory(ies).
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002