text: user2242: 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?
  
  user298: 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:
  >seq1
  MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
  >seq2
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >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<=count[$1];k++){
                  print $1"."k"\t"$2
              }
          }' counts <(FastaToTbl foo.aln) | TblToFasta
  >seq1.1 
  MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
  >seq1.2 
  MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
  >seq1.3 
  MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
  >seq2.1 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.2 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.3 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.4 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.5 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.6 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.7 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.8 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.9 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq2.10 
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  >seq3.1 
  MEEPCS---DPSVEPPQLSQETFSDLRKL--LPENNFLSPLPSQAMCDDL
  >seq3.2 
  MEEPCS---DPSVEPPQLSQETFSDLRKL--LPENNFLSPLPSQAMCDDL
  
  Note that the above assumes your shell supports the <(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 > foo.tbl first, and then use foo.tbl as input.  
  
original_text: 2242: <p>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).</p>
  
  <p>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?</p>
  
  <p>So that when generating the weblogo image it takes into account the abundances of each sequence?</p>
   298: <p>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.</p>
  
  <p>Generate a simple mapping file (<code>counts</code>) with the number of times each sequence was found:</p>
  
  <pre><code>seq1 3
  seq2 10
  seq3 2
  </code></pre>
  
  <p>Then, given an aligned protein fasta file (<code>foo.aln</code>) like this:</p>
  
  <pre><code>&gt;seq1
  MEEPQS---DPSVEPP-LSQETFSDLWKLCFLPENNVLSPLPSQAM-DDL
  &gt;seq2
  MEEPQSCFGDPSVEPPPLSQETFKDLWKL--LCENNVLS---SQAM-DDL
  &gt;seq3
  MEEPCS---DPSVEPPQLSQETFSDLRKL--LPENNFLSPLPSQAMCDDL
  </code></pre>
  
  <p>You can simply repeat the sequences as needed (see my answer <a href="https://bioinformatics.stackexchange.com/a/2651/298">here</a> for the <code>FastaToTbl</code> and <code>TblToFasta</code> commands):</p>
  
  <pre><code>$ 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
  </code></pre>
  
  <p>Note that the above assumes your shell supports the <code>&lt;(command)</code> syntax for <a href="http://www.tldp.org/LDP/abs/html/process-sub.html" rel="nofollow noreferrer">process substitution</a>. 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 <code>FastaToTbl foo.aln &gt; foo.tbl</code> first, and then use <code>foo.tbl</code> as input.  </p>
  