I have a query on perl system command. I would like to learn from perl monks how to place variables inside system command ?

In the script below, program "phylip" generates two output files and asks user to name them. I want to name the first output file as "blah.txt" and second as "blah.xls".

$filename ="blah.doc";
....
....
$filename =~ s/\.doc//;
system 'echo "$filename.txt\n$filename.xls\n" | phylip';
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(blah.doc is the input file, I use at the beginning of a long script)

when I run above script, "phylip" doesn't recongnize either of the filenames. Can anyone advise me, how to go about doing this ?