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     24   next unless defined %{$matches{$fasta_id}};

...
     51           next unless defined @{$matches{$fasta_id}{$sitekey}}
+;

     91   unless (defined @{$sets{$fasta_id}}) {

Use of "defined" on aggregates (hashes and arrays) is deprecated.  It 
+used to report whether memory for that aggregate has ever been alloca
+ted.  This
behavior may disappear in future versions of Perl.  You should instead
+ use a simple test for size:

    if (@an_array) { print "has array elements\n" }
    if (%a_hash)   { print "has hash members\n"   }