Does anyone know a program that quantifies and displays (like in a table format) the differences between aligned sequences?
For ex. I've got 14 aligned DNA sequences, and I'd like to know how many differences are between #1 and #2, #1 and #3, but in a table-like (or Excel-like) format, because I've already done the phylogenetic work.
I didn't find an option like this in MEGA, for example...
You can do this in MEGA. In the section Distance you can choose different settings. If you choose "No. of Differences" you get a table of pariwise differences among all your sequences. This can then be exported in a format readable for Excel etc.
I use a program called MacVector, which allows this sort of comparison. Unfortunately, it is a fairly expensive program, and is only available on a Mac, though I think the company may be planning on a Windows version of the program.
DNAsp shows the number of polymorphic sites among sequences input. I don't know if there are some option for output in a table format, but you can to try. Likewise, you can use any software which to make pairwise aligment using only two sequences for comparing identity and align score. But, in this case, you will need to organize the table by hands.
Thank you all for the replies!
David: Unfortunately, Mac isn't an option for me... Thx anyway!
Sinéad: thx for the tip, the program does indeed have some interesting features. However, I can't seem to find where it does what I'm looking for... I'll continue exploring it.
Gustavo: I'll try it, thx.
Cristine: I know about the pairwise alignment, I was just hoping I could avoid the trouble ;) Because doing that for 14 different sequences, in DNA and protein...
I agree with you, pairwise is hard-working for your goal, but now I don't remember other option...
Actually multiple alignment with CLUSTALX provides this kind of output (matrix) as well. It has been discussed here in another thread already. If this is what you are looking for, please see my answer there (https://www.researchgate.net/post/Sequence_alignment_in_MATLAB)
Heads or Tails: a simple reliability check for multiple sequence alignments http://nsm.uh.edu/~dgraur/scripts/HoT/
Comparison of sequences may be on different factors. Function is one of the most important factors. DNA may not be compared simply in terms of ATGC letters. It require deeper understanding of its transcription and translation factors. The numbers or table you make with out these factors will not solve the purpose. Carbon content and distribution in proteins of these DNA has important role. During evolution the DNA got changed because of this reason.
The PHYLIP DNADIST program does this, and it can compute the pairwise distances according to many models of evolution, from a strict % identity (Hamming distance) to Kimurea 2 parameter (transistions counted differently than transversions) to the GTR (general time-reversible model). DAMBE, BioEdit and many other programs also do this, usually by using the DNADIST code. There are several web servers that run DNADIST such as http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::dnadist if you want to "test drive" before installing PHYLIP for yourself.
You can do this in MEGA. In the section Distance you can choose different settings. If you choose "No. of Differences" you get a table of pariwise differences among all your sequences. This can then be exported in a format readable for Excel etc.
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