How to generate a weblogo image that takes into account sequence frequencies? I have a large aligned amino acid sequences file (fasta file) from next generation sequencing data. 
The unique sequences have been aligned but these all have certain read counts (frequencies associated with them).

I would like to generate a weblogo image that has the true probability of amino acids at each position. 
Is there a way to input frequencies/read counts with the aligned files of sequences using weblogo?
For example, in the title of the fasta file or as a csv/tsv file?

So that when generating the weblogo image it takes into account the abundances of each sequence?
Don't use the unique sequences. The whole point of sequence logos is that the height of the letter represents its frequency at a given position. You remove this information when you make your sequences unique. So, while it makes sense to use unique sequences when aligning, you shouldn't when building your logo.

Generate a simple mapping file (counts) with the number of times each sequence was found:

seq1 3
seq2 10
seq3 2


Then, given an aligned protein fasta file (foo.aln) like this:

&gt;seq1
MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
&gt;seq2
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq3
MEEPCS---DPSVEPPQLSQETFSDLRKL--LPENNFLSPLPSQAMCDDL


You can simply repeat the sequences as needed (see my answer here for the FastaToTbl and TblToFasta commands):

$ awk '
        (NR==FNR){
            count[$1]=$2; 
            next
        } 
        {
            for(k=1;k&lt;=count[$1];k++){
                print $1"."k"\t"$2
            }
        }' counts &lt;(FastaToTbl foo.aln) | TblToFasta
&gt;seq1.1 
MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
&gt;seq1.2 
MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
&gt;seq1.3 
MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
&gt;seq2.1 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.2 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.3 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.4 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.5 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.6 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.7 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.8 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.9 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq2.10 
MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
&gt;seq3.1 
MEEPCS---DPSVEPPQLSQETFSDLRKL--LPENNFLSPLPSQAMCDDL
&gt;seq3.2 
MEEPCS---DPSVEPPQLSQETFSDLRKL--LPENNFLSPLPSQAMCDDL


Note that the above assumes your shell supports the &lt;(command) syntax for process substitution. Bash, the default shell on most Linux and macOSX installations does, but if you are using a shell that doesn't, you might need to run FastaToTbl foo.aln &gt; foo.tbl first, and then use foo.tbl as input.