Per Alastair's comment, I tried MstatX, at https://github.com/gcollet/MstatX.

The program is easy to use and has several ways of calculating the score. However, it bothers me a little that it doesn't output a final score to the termal. It prints a score for each column into a file, which I was able to sum up. It also bothers me that it doesn't come packaged with a simple matrix for DNA and so it is only optimized for protein. I quickly made up a DNA matrix on the spot which may not be technically correct.

tar zxvf gcollet-MstatX-31481c6.tar.gz
cd gcollet-MstatX-31481c6
make
./mstatx -ma path/to/file -b -sp data/dna.mat
perl -e 'while(<>){$score+=$_;}print "$score\n";' < file.cons

The file I made (probably isn't the most correct thing I could have made)

H DNA matrix
D DNA matrix by Lee Katz
R LIT:1902106 PMID:1438297
A Henikoff, S. and Henikoff, J.G.
T Amino acid substitution matrices from protein blocks
J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
* matrix in 1/3 Bit Units
M rows = ATCGN-, cols = ATCGN-
      2.
     -1.      2.
     -1.     -1.      2.
     -1.     -1.     -1.      2.
     -1.     -1.     -1.     -1.     -2.
     -2.     -2.     -2.     -2.     -2.     -2.
//

muscle3.8 has a 'spscore' option which computes an SP objective score for a multiple sequence alignment. e.g. path/to/muscle -spscore file_name

e.g. to extract just the score into a variable (psuedocode):

Compute SP score with muscle (e.g. path/to/muscle -spscore file_name -log <log_file>)
Read log file
Iterate through each line of file
    If line contains string 'SP=' (perl e.g. /SP=/)
        match 'SP=' (perl e.g. =~ /SP=/)
        Print segment after match (perl e.g. print $')

NB: You could even extract the matching line with unix 'grep' Download muscle from: http://www.drive5.com/muscle/

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