If you allow me to complicate my script, The complete system command looks like this...
system 'echo "4\n6\n3\n5\n\n1\n$filename.fsmi\n5\n$filename.phb\n111\n
+1000\n4\n$filename.ph\n$filename.dst\n\n2\n" | phylip';
phylip has many options, and user have to choose the option by pressing 1 or 2 or 3 or 4 ... etc. The point of giving output file name comes after choosing many such options. When I run "phylip" program separately (by "seperately", I mean, running "phylip" outside perl script) I type 1,2 or 3...etc and press ENTER key to choose that option. When I am calling "phylip" inside perl script, I use "\n" as a substitute for ENTER key |