As a beginner, I made all of these mistakes and then some. Thank you chromatic for this excelent node, and dominus for the Red Flag papers. While forcing myself to rewrite a script to have them all  use strict I came up with the following solutions which may be of benefit to others like me (for most of you this is way too trivial, but this is the voice of a beginner).

To access a number of files in a loop construct, this was my initial attempt:

for ($results = 2; $results <34; $results++) {
            my $file="current$results.res";
            open (TALLYRESULTS, ">$file") or die ("cant open results f
+ile");
              ....
            }
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A common mistake, apparently, which turned out to be easy to avoid:

for ($results = 2; $results <34; $results++) {
                my $file="current".$presence.".res";
                ....
                }
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Another (double!) 'Red Flag' situation was this:

 @tree1=@samples[0..2];
  ...  (another 10 of those)
 @tree12=@samples[33..35];
                                        
 for ($z = 1; $z <= 12; $z++) {
 $arrayname="tree$z";
 foreach $patch(@$arrayname) {
       ... do something
       }
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and solving it taught me a thing or two about hashes:

 my %trees = (1 => "@samples[0..2]", 
                          ... (another 10 of these)
                        12 => "@samples[33..35]",
                         );
                        
while ((my $tree, my $samples) = each (%trees) ){
               my @patches = split (/ */, $samples);
                foreach $patch(@patches) {
                             ... do something
                 }
[download]

My script now runs under strict, and I'm proud of it ;-)