You dont need the map, a simple array assignment will do.

my @strings = ($genome1, $genome2);
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Update. That said, if you don't have your strings in an array, and its difficult to put them into one to start with, a small modification to the routine will prevent needless duplication.

#! perl -sw
use strict;
# ... your existing code....

my @strings = \($genome1, $genome2);

my ($total, $p) = (0, 0);
do {
  $total = 0;
#NOTE: Extra $'s v ........................................v
  print substr( $$strings[$_]}, $p, 60 ) . "\n" for 0 .. $#$strings;
  print "\n";
  $p+=60;
  $total += length($_) - $p for @$strings; # And here!
} while( $total > 0 );
__END__
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