The GIF file format is widely described on the internet. One of the better descriptions is here.

This piece of code tweaks the global colour table (simply reversing the indexes):

#! perl -slw
use strict;

open GIF, '<:raw', $ARGV[ 0 ] or die $!;
my $gif = do{ local $/; <GIF> };
close GIF;

## Extract the colour table
my @GCT = unpack '(A3)256', substr $gif, 13, 256 * 3;

## SWap the colours end to end
@GCT = reverse @GCT;

## put the colour table back
substr( $gif, 13, 256*3 ) = pack '(A3)256', @GCT;

open OUT, '>:raw', 'modified.gif' or die $!;
print OUT $gif;
close OUT;
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To do things properly, you would need to check the size of the colour table entry (see byte 10-bits 4..7 of the header) and account for colour tables that use less that 24-bits per entry. Also, you should check bit-0 of the same byte to determine if global or local colour tables are in use, but the code may get you started.