You wrote

qq(echo "$filename.txt\n$filename.xls\n" | phylip );
qq~echo "$filename.txt\n$filename.xls\n" | phylip ~;
[download]

Your script would have been

system qq(echo "$filename.txt\n$filename.xls\n" | phylip );
system qq~echo "$filename.txt\n$filename.xls\n" | phylip ~;
[download]

I made a mistake by running your script blindly, so it didn't work that time. Yes you are right, single quotes do not interpolate, I needed double quotes !

Thank you :-)