I'm sorry if I made waste your time but (as I replied above) it wasn't possible for me to copy&paste the code. Also I thought it was really basic error that didn't require running to sort out since the problem is I don't know very well how to use references to functions.But I thank you for trying to fix it anyway, not everybody would do that. If the actual code is more usefull for you here it is:

#!/usr/bin/perl

$fileName   = $ARGV[0];
$windowSize = $ARGV[1];
$windowIncrement = $ARGV[2];

open(CPF, $fileName) or die ("Can't open file ", $fileName);
@lines = <CPF>;
close (CPF) or warn ("Unable to close ", $fileName);
$n = @lines;

$index = 0;
@allNames;
@allSeq;
$nbTaxa;
$nbGenes;
#$lastLine = "start";

$alternatingIter = sub {return $_[0]};
$followedIter = sub {return (($_[0] % 10) - 1) };
$iter;

chop $lines[0];
($nbTaxa,$nbGenes)=split / +/, $lines[0];    

&sorter ($lines[1]);


    if (((length $second) == 0) && ($first =~ /[AGTC]+/)){    
        $iter = $followedIter;
        chop ($first);
        $allSeq[$index]= $allSeq[$index].$first;

        print "TYPE: just sequence  -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }


    elsif (((length $second) > 0) && ($first =~ /(\w)+/) &&  ($second 
+=~ /[AGTC]+/) ){    
        $iter = $alternatingIter;
        $allNames [$index] = $first;
        chop ($second);
        $allSeq [$index] = $second;
        $index++;

        print "TYPE: name + sequence -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }

foreach $tmp (@lines[3..@lines]){
    &sorter ($tmp);
}


sub sorter {
    $tmp = $_[0];
    ($first, $second)= split / +/, $tmp;

    if (((length $second) == 0) && ($first =~ /[AGTC]+/)){    
        chop ($first);
        $allSeq[$index]= $allSeq[$index].$first;

        print "TYPE: just sequence  -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }


    elsif (((length $second) > 0) && ($first =~ /(\w)+/) &&  ($second 
+=~ /[AGTC]+/) ){    
        $allNames [$index] = $first;
        chop ($second);
        $allSeq [$index] = $second;
        $index++;

        print "TYPE: name + sequence -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }
    elsif($first eq "\n"){
        print "TYPE: do nothing -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }
    else{
        print "TYPE: you have a problem with the format of file".$file
+Name." -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }
    print "index: ".$index."\n";
}
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I've cutted the parts that don't have anything to do with the problem so I'm almost certain it will run. Still, the problem is the same (using the iter reference) as i didn't understand what you fixed.