Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-22T17:18:38.273Z
Answers.LastActivityDate: 2021-11-22T17:18:38.273Z
Answers.UserDisplayName: Stas Malavin
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-22T21:11:00.473Z
Answers.LastActivityDate: 2021-11-22T21:11:00.473Z
Answers.UserDisplayName: Chris_Rands
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-30T15:00:01.443Z
Answers.LastActivityDate: 2021-11-30T15:00:01.443Z
Answers.UserDisplayName: Colin D
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-22T04:05:31.787Z
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Answers.LastEditDate: 2021-11-22T04:11:41.880Z
Answers.UserDisplayName: Maximilian Press
Body: <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>
  
Tags: <phylogenetics><multiple-sequence-alignment>
Title: Remove gaps from alignment?
ThreadText: # Remove gaps from alignment?
  
  (Asked by: username_0 on 2021-11-22)
  
  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.
  
  **Tags:** phylogenetics, multiple-sequence-alignment
  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_1 on 2021-11-22. Score: 3
  
  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](https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropy/) and also installable from [Bioconda](https://anaconda.org/bioconda/bmge).
  
  
  ---
  
  ### Answer by username_2 on 2021-11-22. Score: 2
  
  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](https://academic.oup.com/mbe/article/27/8/1759/988930), 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
  
  
  ---
  
  ### Answer by username_3 on 2021-11-30. Score: 1
  
  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>
  
  
  ---
  
  ### Answer by username_4 on 2021-11-22. Score: 1
  
  [Gblocks](https://academic.oup.com/mbe/article/17/4/540/1127654) is a tool for removing gaps/poorly conserved positions from alignments. Available [here](http://molevol.cmima.csic.es/castresana/Gblocks.html). [Here is a webserver](http://molevol.cmima.csic.es/castresana/GBLOCKS_server.html) that runs it for you.
  
  It's a bit old, possibly there are others at this point.
  
  
  ---
  
  