So, can any monk would suggest me any better way to write this code that is more robust, with use strict'.

Update: fixed an edge case in sub read_file.

#!/usr/bin/perl
use warnings;
use strict;

use GD;


my ( $min1, $max1, $x1, $y1, $lines ) = read_file( 'fwd.stb' );

# Define constants
my $X1start = 50 + 20;               # X-axis
my $Y1start = 300;                   # X-axis
my $X1end   = 450 + $lines - 400;    # X-axis
my $Y1end   = 300;                   # X-axis
my $X2start = 50 + 20;
my $Y2start = 100;
my $X2end   = 50 + 20;
my $Y2end   = 300;

# create a new image
my $im = new GD::Image( $X1end + 50, $Y2end + 100 );

# allocate some colors
my $white = $im->colorAllocate( 255, 255, 255 );
my $green = $im->colorAllocate( 0,   255, 0 );
my $black = $im->colorAllocate( 0,   0,   0 );
my $red   = $im->colorAllocate( 255, 0,   0 );
my $blue  = $im->colorAllocate( 0,   0,   255 );


my $half_lines = int( $lines / 2 );
# set the caption for the graph
$im->string( gdLargeFont, $half_lines - 50, 20, 'ENERGY GRAPH', $black
+ );

# draw the y-axis & x-axis
$im->line( $X2start, $Y2start, $X2end, $Y2end, $black );
$im->line( $X1start, $Y1start, $X1end, $Y1end, $black );

# set the caption for x-axis and y-axis
$im->string(   gdLargeFont, $half_lines - 50, 335, 'NUCLEOTIDE POSITIO
+N', $black );
$im->stringUp( gdLargeFont, 5, 260, 'FREE ENERGY(delta G)', $black );

$im->string( gdSmallFont, $half_lines + 100, 20, ' Genomic  Sequence -
+------', $red );
$im->string( gdSmallFont, $half_lines + 100, 40, ' Shuffled Sequence -
+------', $blue );


my ( $min2, $max2, $x2, $y2 ) = read_file( 'total_shuffle.stb' );


my $min = $min1 <= $min2 ? $min1 : $min2;
my $max = $max1 >= $max2 ? $max1 : $max2;

graph( $x1, $y1, $min, $max );


open my $DISPLAY, '|-:raw', 'display', '-' or die "Cannot open pipe to
+ 'display' $!";
print $DISPLAY $im->png;
close $DISPLAY or warn $! ? "Error closing 'display' pipe: $!" : "Exit
+ status $? from 'display'";

exit 0;


sub read_file {
    my $file_name = shift;

    open my $fh, '<', $file_name or die "Cannot open '$file_name' $!";

    my ( $min, $max, @x, @y );
    while ( <$fh> ) {
        my @value = split;
        push @x, $value[ 0 ] - 7;
        push @y, $value[ 1 ];

        if ( @y > 1 ) {
            $max = $y[ -1 ] if $max < $y[ -1 ];
            $min = $y[ -1 ] if $min > $y[ -1 ];
            }
        elsif ( @y == 1 ) {
            $min = $max = $y[ -1 ];
            }
        }

    return $min, $max, \@x, \@y, $.;
    }

sub graph {
    my ( $x_ref, $y_ref, $minEnergy, $maxEnergy ) = @_;

    # Scaling the values
    my $Yscale = ( $Y2end - $Y2start ) / ( abs( $minEnergy ) - abs( $m
+axEnergy ) );

    my $scale = ( $minEnergy - $maxEnergy ) / 5;

    my $incEnergy = $maxEnergy;
    while ( $incEnergy > $minEnergy ) {   ##### Prob loop####

        my $x1 = $X1start - 2;
        my $y1 = int( ( ( abs( $incEnergy ) - abs( $maxEnergy ) ) * $Y
+scale ) + $Y2start );
        my $x2 = $X1start + 2;

        $im->line( $x1, $y1, $x2, $y1, $black );
        my $displayEnergy = sprintf '%2.1f', $incEnergy;
        $im->string( gdSmallFont, $x1 - 35, $y1 - 10, $displayEnergy, 
+$black );
        $incEnergy = $incEnergy + $scale;
        }

    # mark 10 points on the position axis
    my $posSkip = int( @$x_ref / 10 );
    # If the length of the fragment is lesser than the x-axis

    my $skipPixel = ( $X1end - $X1start ) / @$x_ref;

    my $count;
    for my $i ( 0 .. $#$x_ref - 1 ) {
        my $x1 = int( $i * $skipPixel + $X1start );
        my $y1 = int( ( abs( $y_ref->[ $i ] ) - abs( $maxEnergy ) ) * 
+$Yscale + $Y2start );
        my $x2 = int( ( $i + 1 ) * $skipPixel + $X1start );
        my $y2 = int( ( abs( $y_ref->[ $i + 1 ] ) - abs( $maxEnergy ) 
+) * $Yscale + $Y2start );

        $im->line( $x1, $y1, $x2, $y2, $red );
        $count++;

        if ( $count == $posSkip ) {
            $x1 = int( $i * $skipPixel + $X1start );
            $y1 = $Y1end - 2;
            $x2 = int( $i * $skipPixel + $X1start );
            $y2 = $Y1end + 2;

            $im->line( $x1, $y1, $x2, $y2, $black );
            $im->string( gdSmallFont, $x1, $y1 + 10, $i + 1, $black );
            $count = 0;
            }
        }
    }

__END__
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