Does anybody know a good manual editor of multiple sequence alignments. I have been using Genedoc for ages but it really molests me that it doesn't have an undo function, besides some other small flaws. What is should at least do is insert/remove gaps in a sequence (or in all other sequences), drag, slide, manual editing of residues. Nice would be if has a function to group sequences (and work on the subgroup only). Then it should have all the typical formatting options for publication.
SeaView is a good editor, though it has some bugs also and crashes sometimes, I do recommend it for this kind of editing.
The JalView application supports alignment editing reasonably well and implements most of the features you mention (see http://www.jalview.org/help/html/editing/index.html). Just be sure to use the application (see http://www.jalview.org/download.html) rather than the applet.
There are many MSA editors, and the choice is largely a matter of personal taste, so see some of the many lists of possible tools:
I use Mesquite. It has all the features you mention, except perhaps formatting for publication, depending on what you need there. The gap insertion, deletion, etc., is just done by choosing a appropriate tool, selecting blocks of the matrix, and sliding.
The main drawback is that there are a lot of other functions to the program, so its a little hard to find your way around.
BioEdit is probably the single best tool except that it is no longer being supported. I believe there was such a tool in the Wisconsin package as well. Sequencher also provides some good tools.
The real issue is what manual editing is being used for, however. I'm not sure that the community has produced a good MSA program that duplicates the key functions of most manual MSA editing... if it has, I don't know about it. Those functions would allow locking in 'what is known' - reference alignments, boundaries of coding regions and annotated regulatory sequences, etc - so that coding regions are aligned by codon preferentially, for example, while adjacent non-coding regions are not; also it would take quality scores and reference trees, cases where reads come from the same region of the same template, for minor 'assembly' solving.
Hopefully this suite of functions would largely supplant manual editing and especially Sanger base calling.
I have used XCed for more than 10 years: http://align.bmr.kyushu-u.ac.jp/xced/ originally because I was in the group where this alignment editor was initially developed, but even after trying several others I cannot switch to any other program.
Base-By-Base Java tool http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/
Handles protein, DNA seq , genomes, see annotation, add comments, highlights difference between sequences, shows reading frames Ask if you need more help. Chris Upton
see: Base-By-Base: single nucleotide-level analysis of whole viral genome alignments. Brodie R, Smith AJ, Roper RL, Tcherepanov V, Upton C. BMC Bioinformatics. 2004 Jul 14;5:96. PMID: 15253776
Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments William Hillary, Song-Han Lin, Chris Upton BMC: Microbial Informatics and Experimentation 2011, 1:2 (14 June 2011)
Jalview www.jalview.org) now have a wide range of Jalview Online Training videos on YouTube that might help you. As well as a playlist on Selecting and Editing Sequences, they are playlist on Getting Started and Colour, Appearance and Figure Generation