The system command allows the user to run programs outside of mothur without leaving the mothur environment. This command is useful for changing directories and renaming files. The syntax for this command is different from the other commands - the actual command that needs to be run should be placed within the parentheses. If you are unfamiliar with shell programs you might familiarize yourself with the different mac/linux and windows shell programs that are available.
To copy a file in the Mac/Linux environment:
mothur > system(cp esophagus.unique.bad.accnos esophagus.bad.accnos)
To copy a file in the Windows environment:
mothur > system(copy esophagus.unique.bad.accnos esophagus.bad.accnos)
To mock someone in the Mac environment:
mothur > system(say -v Vicki joe smells)
1.46.0 - Simplifies system command. #782