What to use to edit RNA alignments? 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                 &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
//
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!)