text: user14001: I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each.
  Here is a rough workflow for generating the reads:
  
  Expression of a library of sequence variants for a heterogeneous protein of interest in phage.
  Selection of high-fitness variants according to a custom assay.
  Extraction of the variant pool via amplification of the variable region of the gene of interest.
  Preparation of Illumina sequencing library from the amplicon pool.
  Deep sequencing of the amplicon pool.
  
  I've already combined the paired-end reads with USearch and manually removed sequences with subpar quality scores, but I now need to translate all of the remaining DNA sequences into amino acid sequences. I'm uncertain of where to begin addressing this issue, and I was hoping someone could point me in the direction of an application or python package that could assist me.
  My goal: Count the abundances of each sequence variant within the Illumina data to identify which of the protein sequences are the most fit.
  
  user2108: Based on back and forth in the comments, I think that you might be interested in a deep mutational scanning workflow, for example dms_tools2 or enrich2.
  These are built specifically for the kind of experiment that you are interested in, if I understand correctly. See attached figure from dms_tools2:
  
  
original_text: 14001: <p>I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each.</p>
  <p>Here is a rough workflow for generating the reads:</p>
  <ol>
  <li>Expression of a library of sequence variants for a heterogeneous protein of interest in phage.</li>
  <li>Selection of high-fitness variants according to a custom assay.</li>
  <li>Extraction of the variant pool via amplification of the variable region of the gene of interest.</li>
  <li>Preparation of Illumina sequencing library from the amplicon pool.</li>
  <li>Deep sequencing of the amplicon pool.</li>
  </ol>
  <p>I've already combined the paired-end reads with USearch and manually removed sequences with subpar quality scores, but I now need to translate all of the remaining DNA sequences into amino acid sequences. I'm uncertain of where to begin addressing this issue, and I was hoping someone could point me in the direction of an application or python package that could assist me.</p>
  <p>My goal: <strong>Count the abundances of each sequence variant within the Illumina data to identify which of the <em>protein</em> sequences are the most fit.</strong></p>
   2108: <p>Based on back and forth in the comments, I think that you might be interested in a deep mutational scanning workflow, for example <a href="https://jbloomlab.github.io/dms_tools2/examples.html" rel="nofollow noreferrer"><code>dms_tools2</code></a> or <a href="https://github.com/FowlerLab/Enrich2" rel="nofollow noreferrer"><code>enrich2</code></a>.</p>
  <p>These are built specifically for the kind of experiment that you are interested in, if I understand correctly. See attached figure from dms_tools2:</p>
  <p><a href="https://i.stack.imgur.com/07tZ9.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/07tZ9.png" alt="enter image description here" /></a></p>
  