text: user12135: I have an MSA (protein sequence) and I have used various programmes (Clustal, Aliview, MEGA11 etc) to align. However, in all programmes I get many gaps which is not ideal as I am trying to construct a tree from this alignment.
  My question is are there any tools to delete gaps in alignments?
  Your help would be greatly appreciated.
  
  user2108: Gblocks is a tool for removing gaps/poorly conserved positions from alignments. Available here. Here is a webserver that runs it for you.
  It's a bit old, possibly there are others at this point.
  
  user60: This new tool, CIAlign, talks about some automated removal of gaps in multiple sequence alignments
  https://twitter.com/thekatybrown1/status/1306215132670889984
  https://github.com/KatyBrown/CIAlign
  
  user2574: You may also find useful the BMGE tool (stands for Block Mapping and Gathering with Entropy). BMGE selects regions in a multiple sequence alignment that are suitable for phylogenetic inference by computing their entropy-like score. This allows to distinguish among biologically expected and unexpected variability for each aligned character. BMGE also implements different types of trimming (for instance, deletes gaps) to minimize phylogeny reconstruction artifacts.
  Available from here and also installable from Bioconda.
  
  user104: If you want an ungapped alignment, you could do an ungapped alignment (the older read aligners were ungapped, e.g. bowtie). However, I suggest that you don't want an ungapped alignment, you just want a stricter one, here's a few options...
  
  Remove/trim poorly aligning sequences. You could try GUIDANCE, which has an explicit model or GBLOCKS for a more simple filtering criteria
  Tune your alignment parameters for ClustalOmega/MAFFT etc. to make it stricter
  Finally, consider that your sequences must be homologous otherwise you'll trim away sequences until you have a random alignment that appears good
  
  
original_text: 12135: <p>I have an MSA (protein sequence) and I have used various programmes (Clustal, Aliview, MEGA11 etc) to align. However, in all programmes I get many gaps which is not ideal as I am trying to construct a tree from this alignment.</p>
  <p>My question is are there any tools to delete gaps in alignments?</p>
  <p>Your help would be greatly appreciated.</p>
   2108: <p><a href="https://academic.oup.com/mbe/article/17/4/540/1127654" rel="nofollow noreferrer">Gblocks</a> is a tool for removing gaps/poorly conserved positions from alignments. Available <a href="http://molevol.cmima.csic.es/castresana/Gblocks.html" rel="nofollow noreferrer">here</a>. <a href="http://molevol.cmima.csic.es/castresana/GBLOCKS_server.html" rel="nofollow noreferrer">Here is a webserver</a> that runs it for you.</p>
  <p>It's a bit old, possibly there are others at this point.</p>
   60: <p>This new tool, CIAlign, talks about some automated removal of gaps in multiple sequence alignments</p>
  <p><a href="https://twitter.com/thekatybrown1/status/1306215132670889984" rel="nofollow noreferrer">https://twitter.com/thekatybrown1/status/1306215132670889984</a></p>
  <p><a href="https://github.com/KatyBrown/CIAlign" rel="nofollow noreferrer">https://github.com/KatyBrown/CIAlign</a></p>
   2574: <p>You may also find useful the BMGE tool (stands for Block Mapping and Gathering with Entropy). BMGE selects regions in a multiple sequence alignment that are suitable for phylogenetic inference by computing their entropy-like score. This allows to distinguish among biologically expected and unexpected variability for each aligned character. BMGE also implements different types of trimming (for instance, deletes gaps) to minimize phylogeny reconstruction artifacts.</p>
  <p>Available from <a href="https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropy/" rel="nofollow noreferrer">here</a> and also installable from <a href="https://anaconda.org/bioconda/bmge" rel="nofollow noreferrer">Bioconda</a>.</p>
   104: <p>If you want an ungapped alignment, you could <em>do</em> an ungapped alignment (the older read aligners were ungapped, e.g. bowtie). However, I suggest that you don't want an ungapped alignment, you just want a stricter one, here's a few options...</p>
  <ul>
  <li>Remove/trim poorly aligning sequences. You could try <a href="https://academic.oup.com/mbe/article/27/8/1759/988930" rel="nofollow noreferrer">GUIDANCE</a>, which has an explicit model or GBLOCKS for a more simple filtering criteria</li>
  <li>Tune your alignment parameters for ClustalOmega/MAFFT etc. to make it stricter</li>
  <li>Finally, consider that your sequences must be homologous otherwise you'll trim away sequences until you have a random alignment that appears good</li>
  </ul>
  