Question: Manual Msa Editor
3
gravatar for Arjen Ten Have
8.1 years ago by
Mar del Plata Argentina
Arjen Ten Have350 wrote:

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.

alignment multiple • 4.2k views
ADD COMMENTlink modified 3.9 years ago by Suzanne70 • written 8.1 years ago by Arjen Ten Have350
2
gravatar for SES
8.1 years ago by
SES8.3k
Vancouver, BC
SES8.3k wrote:

SeaView is a good editor, though it has some bugs also and crashes sometimes, I do recommend it for this kind of editing.

Jalview is also very good, and UGENE and (I believe) MEGA also give you this functionality, in addition to a lot of other analysis tools.

ADD COMMENTlink written 8.1 years ago by SES8.3k
1

Seaview appears to have gap insert but I cannot find find out how to remove. Shift - does not do the job (or_ if you wish) Jalview does not allow much in terms of editing UGENE might be an option MEGA I don't trust because of the hopelessly poor phylogeny algorithms it has. Should give it a try though for the editing part. I ll try UGENE and MEGA and hope for the best

Thanks!

ADD REPLYlink written 8.1 years ago by Arjen Ten Have350
1

I just use SeaView for editing personally, that is why I listed it first. To remove bases, just select a sequence ID in the left panel then click the "Edit" menu, then click "Edit sequence" from the menu. From there, you can edit the sequence any way you want. Save the edits, and then the modified sequence will appear in the alignment view.

ADD REPLYlink written 8.1 years ago by SES8.3k
1

I just downloaded and tried Jalvlew. I was pleased but when I scrolled the sequences to the right, I got a major graphical glitch making the sequences unreadable. I use Ubuntu 11.04 64-bit. Anyone having a similar problem?

ADD REPLYlink modified 7.6 years ago • written 7.6 years ago by Eric Normandeau10k
2
gravatar for Priyabrata
8.1 years ago by
Priyabrata70
Priyabrata70 wrote:

Go for Bioedit

http://www.mbio.ncsu.edu/bioedit/bioedit.html

ADD COMMENTlink written 8.1 years ago by Priyabrata70
1
gravatar for Hamish
8.1 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

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:

ADD COMMENTlink modified 6 months ago by RamRS26k • written 8.1 years ago by Hamish3.1k
1
gravatar for Cliff Beall
8.1 years ago by
Cliff Beall450
Ohio
Cliff Beall450 wrote:

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.

http://mesquiteproject.org

ADD COMMENTlink written 8.1 years ago by Cliff Beall450
1
gravatar for dimkal
8.1 years ago by
dimkal730
United States
dimkal730 wrote:

jalview in my opinion is superior to any other tools. Also it's kept up to date with recent updates.

ADD COMMENTlink written 8.1 years ago by dimkal730
1
gravatar for Ben
8.0 years ago by
Ben10
Ben10 wrote:

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.

ADD COMMENTlink written 8.0 years ago by Ben10
1
gravatar for Shigehiro Kuraku
8.0 years ago by
Shigehiro Kuraku10 wrote:

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.

ADD COMMENTlink modified 6 months ago by RamRS26k • written 8.0 years ago by Shigehiro Kuraku10
1
gravatar for Arjen Ten Have
8.0 years ago by
Mar del Plata Argentina
Arjen Ten Have350 wrote:

Looking at all the answers and some manuals I ll go for Bioedit...

ADD COMMENTlink written 8.0 years ago by Arjen Ten Have350
1
gravatar for cupton
8.0 years ago by
cupton10
cupton10 wrote:

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)

ADD COMMENTlink modified 6 months ago by RamRS26k • written 8.0 years ago by cupton10
1
gravatar for Suzanne
3.9 years ago by
Suzanne70
Dundee, Scotland
Suzanne70 wrote:

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

ADD COMMENTlink written 3.9 years ago by Suzanne70
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