Thanks Philip Bailey.
I put up a simplified script in my query, but the actual script is different. It is given below. (Description of this script is in Re^4 above)
As suggested by you, I modified script
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';
system "echo -e \"4\\n6\\n3\\n5\\n\\n1\\n\"$filename.fsmi\"\\n5\\n\"$f
+\\n\\nx\\n\" | phylip" ;
I did not get any error message, but, none of the choices are recognized
I appreciate your help, thank you
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