text: user682: I have many alignments from Rfam Database, and I would like to edit them. 
  I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ? 
  e.g. Stockholm Alignment of Pistol (just few entries). 
  FP929053.1/1669026-1668956   AGUGGUCACAGCCACUAUAAACA-GGGCUU-UAAGCUGUG-AGCGUUGACCGUC----------ACAA-----CGGCGGUCAGGUAGUC
  AFOX01000025.1/1981-1912     ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UUCGGUGAGGUUGGC
  HE577054.1/3246821-3246752   ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UGCGGUGAGGUUGGC
  CP000154.1/3364237-3364168   GUUCGUCUGAGCGAACGCAAACA-GGCCAU-UAAGCUCAG-AGCGUUCACUGGA----------UUCG------UCCAGUGAGAUUGGC`
  `#=GC SS_cons                 <<<<__AAAAA_>>>>-------..<<<<-.----aaaaa.----<<<<<<<<<..........____....._>>>>>>>>>-->>>>`
  `#=GC RF                      acUCGUCuggGCGAguAUAAAuA..cgCaU.UAgGCccaG.AGCGUcccggcgg..........uUau.....uccgccgggGGUuGcg
  //
  
  
  user298: There's nothing really special about RNA alignments, you can use any alignment editor, including whichever one you use for protein. That said, a classic and very useful tool for this sort of thing is JalView. It can be installed locally or run as a Java webapp from your browser.
  
  Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.
  
  
  
  user640: I would suggest use RALEE—RNALignment Editor in Emacs. It can get for you the consensus secondary structure, you can move left/right sequences and their secondary structures (you can't do it in JalView!), and more.
  It's an Emacs mode, so could be a bit hard to start off, but just try, you don't have to use all Emacs features to edit your alignments! 
  
  The RALEE (RNA ALignment Editor in Emacs) tool provides a simple
    environment for RNA multiple sequence alignment editing, including
    structure-specific colour schemes, utilizing helper applications for
    structure prediction and many more conventional editing functions.
  
  Sam Griffiths-Jones Bioinformatics (2005) 21 (2): 257-259.
  
  
  Fig. You can move left/right sequences and their secondary structures (you can't do it in JalView!)
  
original_text: 682: <p>I have many alignments from Rfam Database, and I would like to edit them. 
  I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ? </p>
  
  <p>e.g. Stockholm Alignment of Pistol (just few entries). </p>
  
  <pre><code>FP929053.1/1669026-1668956   AGUGGUCACAGCCACUAUAAACA-GGGCUU-UAAGCUGUG-AGCGUUGACCGUC----------ACAA-----CGGCGGUCAGGUAGUC
  AFOX01000025.1/1981-1912     ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UUCGGUGAGGUUGGC
  HE577054.1/3246821-3246752   ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UGCGGUGAGGUUGGC
  CP000154.1/3364237-3364168   GUUCGUCUGAGCGAACGCAAACA-GGCCAU-UAAGCUCAG-AGCGUUCACUGGA----------UUCG------UCCAGUGAGAUUGGC`
  `#=GC SS_cons                 &lt;&lt;&lt;&lt;__AAAAA_&gt;&gt;&gt;&gt;-------..&lt;&lt;&lt;&lt;-.----aaaaa.----&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;..........____....._&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;--&gt;&gt;&gt;&gt;`
  `#=GC RF                      acUCGUCuggGCGAguAUAAAuA..cgCaU.UAgGCccaG.AGCGUcccggcgg..........uUau.....uccgccgggGGUuGcg
  //
  </code></pre>
   298: <p>There's nothing really special about RNA alignments, you can use any alignment editor, including whichever one you use for protein. That said, a classic and very useful tool for this sort of thing is <a href="http://www.jalview.org/" rel="noreferrer">JalView</a>. It can be installed locally or run as a Java webapp from your browser.</p>
  
  <blockquote>
    <p>Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.</p>
  </blockquote>
  
  <p><a href="https://i.stack.imgur.com/I76Yq.png" rel="noreferrer"><img src="https://i.stack.imgur.com/I76Yq.png" alt="jalview image"></a></p>
   640: <p>I would suggest use RALEE—RNALignment Editor in Emacs. It can get for you the consensus secondary structure, you can move left/right sequences and their secondary structures (you can't do it in JalView!), and more.</p>
  
  <p>It's an Emacs mode, so could be a bit hard to start off, but just try, you don't have to use all Emacs features to edit your alignments! </p>
  
  <blockquote>
    <p>The RALEE (RNA ALignment Editor in Emacs) tool provides a simple
    environment for RNA multiple sequence alignment editing, including
    structure-specific colour schemes, utilizing helper applications for
    structure prediction and many more conventional editing functions.</p>
  </blockquote>
  
  <p><a href="https://doi.org/10.1093/bioinformatics/bth489" rel="nofollow noreferrer">Sam Griffiths-Jones Bioinformatics (2005) 21 (2): 257-259.</a></p>
  
  <p><a href="https://i.stack.imgur.com/XOWVV.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/XOWVV.png" alt="enter image description here"></a></p>
  
  <p><a href="https://i.stack.imgur.com/UPcwI.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/UPcwI.png" alt="enter image description here"></a>
  Fig. You can move left/right sequences and their secondary structures (you can't do it in JalView!)</p>
  