How to generate a weblogo image that takes into account sequence frequencies?
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.