sub filter_by_Species()
# Don't use prototypes unless you NEED them. And even then, you probably don't.


open( NEWALIGN, "<blast_files/$newBlastFile") || die "$!";
#use lexical filehandles and three argument opens to prevent
# obscure bugs. The || is very high precedent. Not wrong
# really, but unecessarily powerful.

#read results file one line at a time
my @resultLine = <NEWALIGN>;
# Arggh. Read entire file into an array at once.

my @subjects = [];  # reference to empty array
# nope. Array whose first element is a reference to an empty array

#so I produce a hash with key = >gi line of report and value = all lines after until next >gi
# I saw no "greater than" in the example data...

for (my $i = 0 ; $i<scalar @resultLine; $i++)
# C style loops. Avoid unless necessary. They work ok but 
# clutter up the script and make it harder figure out what 
# you are doing.

    if ($resultLine[$i] =~ /^>/)
# again, no "greater than" in the example data...

    {
        $current_subject = $resultLine[ $i ];
        chomp ($current_subject);
        push (@subjects, $current_subject);
        $alignment->{$current_subject} = "";
        $alignment->{$current_subject}.$resultLine[ $i ];
}
# you never use the %$alignment hash anywhere so why bother? 

my @elements;
my $boolean;
# declare variables in the smallest scope possible

foreach my $z (@subjects)
{
    chomp $z;
# already chomped in previous loop

    show_Output($boolean, $z, @elements);
# boolean ALWAYS equal 0. Why not just pass 0?