DNA multiple sequence alignment quality check software advise

Question

[cara78]

Hello,

I want to do quality check on my multiple sequence alignment which is in DNA. There are a number of these software for protein but hard to find a good one for DNA. I want to see if the alignment is good and if bad then tell me so I can remove it. That sort of thing.

Does anyone know of any good software the can do quality check on multiple sequence alignment which is in DNA?

[cyril-cros]

I am not sure you can do quality checks on non experimental data. You have a huge number of software offering to do alignments (TCoffee, ClustalOmega,...).

A better question would be, what is your end goal with this multiple alignment: phylogeny and clustering, homology modelling, looking for conserved motifs, doing population genetics? You will have to choose how stringent you want your alignment to be.

Next, what type of sequence do you have (bacterial, eukariotes)?

You can always view your alignment using something like Jalview or Seaview, and check the percentage of conserved nucleotide.

[cara78]

I want to do phylogeny and they are all eukaryotes. I made the MSA with clustal omega.

Answer 1

[Brice Sarver]

Jalview for visualizing your alignment.

GBlocks for removing regions that are difficult to align.

The alignment algorithms will produce the best alignment given a set of criteria and score values (match/mismatch/gap insertion). There is no one way to do a bunch of alignments and check for the best one besides by eye and using some additional information, like protein structure or coding frame. The standard suite of programs (Muscle, MAFFT, Mauve, etc.) will be useful for generating good alignments.