I would like to make suggestions for this code. I just started with the UI. A small problem is that $0 is not a portable name for the current program name. I show below how to make $0 portable.

I think a bigger problem is this use of opts. The normal command line usage for an option like "-l" means that I want the "l" option. If I don't mention -l, that means "no". This idea of -l Y or -l N doesn't make sense, just -l means "yes, I want -l" and no mention of -l means "no -l".

Below is a standard design pattern for a command line I/F.

#!/usr/bin/perl -w
use strict;

use Getopt::Std;
use Data::Dumper;
use File::Basename;
my $prog_name = basename($0);

my $usage = <<"USAGE";
Usage: $prog_name [-flags] <fasta file> <output file> 

 Files must be all one type. ie (all fasta NT, all fastq, all fasta fn
+a).
 The script is able to detect if fasta or fastq files have been suplie
+d. 
 Depending on the flags, it produces different output.

$prog_name will produce a histogram, a vector distribution, and 
a NT/AA distribution. 

For fastq files, you must use a flag to specify which version.
of fastq the file is formatted with.

-l to specify Solexa/Illumina < 1.3 Fastq 
-s to specify Sanger Fastq
-u to specify Illumina >= 1.3 Fastq
only one option is allowed!
USAGE

###### "code" starts here ###########
my %opts;
die "$usage" if !getopts ("lsu", \%opts);

# above removes any -lu or -lus options from command line
# all that is left in @ARGV are the two file paths...
# above will cause $usage to be printed if unknown option, say
# "-x" is encountered.

die "must have 2 files: fasta infile and an output file!\n$usage"
     if (my ($inflile, $outfile) = @ARGV) !=2;

foreach my $opt (keys %opts)  #just for debugging....
{
   print "$opt= $opts{$opt}\n";
}

# here is where you put stuff that rules out combos of options.
# I am guessing that more than one option is not right
die "only one option allowed!\n$usage"
    if (keys %opts >1); #ie only 0 or 1 options are allowed

#now open the input file and the output files
#
#error should say "can't open $infile for read", etc....
#we are past the usage stuff...
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Definitely DO NOT DO THIS!

open STDERR, ">/dev/null";
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That sends error output from like "die" to the "bit bucket"!