system 'echo "r\ny\nr" | phylip sub_program_1';

Hurray... it runs perfectly well :-) Your observation, to include "\n" after each alphabet is correct way to run "phylip"

you wrote in Re^3..

Try

system 'echo "rYr" | phylip sub_program_1';
or
system 'echo -e "r\nY\nr" | phylip sub_program_1';
[download]

By giving "\n" and "- e", "phylip" was overfed. So, It didn't work that time.

After you have explained function of "-e" and "-n" in Re^5, I removed "-e" and it worked perfectly well.

I appreciate your help,

Cheers

Chak