Strange. Works for me:

perl -e '$nameWithoutFastaSign = ">1elwA";
         print "before: $nameWithoutFastaSign\n";
         $nameWithoutFastaSign =~ tr/>//d;
         print "after: $nameWithoutFastaSign\n";'
[download]

Output:

before: >1elwA
after: 1elwA
[download]