From the Phylip FAQ - "Why didn't it occur to you to allow the options to be set on the command line?"
You may be asking this question because you want to automate the
operation of PHYLIP programs using batch files (command files) to run
in background. If that is the issue, see the section of this main
documentation page on "Running the programs in background or under
control of a command file".
While PHYLIP supports this via command-scripts (see the other answers for ways of dealing with this), command-line support can be found in the EMBOSS EMBASSY package PHYLIPNEW.
If you are using a Debian based Linux distribution this can be installed via the embassy-phylip package (my be installed by the med-bio and science-biology meta-packages). Other distributions may also have ports, or you can always build from source (see "Downloading EMBOSS").