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Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment?

How big is the need for better algorithms? How many sequences need to be alignment in a typical test? I am trying to understand how important problem this is in bioinformatics.

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This would be better asked on biostars.org, the bioinformatics stack exchange. For the typical number of sequences aligned: you cannot say that. There are so many different uses of MSAs and too many different datasets one could have to be able to give one typical example. –  skymninge Jul 30 at 8:51
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@skymninge Bioinformatics are on-topic here, and Biostars is not affiliated with SE in any way now (it was a SE 1.0 site, which means they used the SE software but SE wasn't involved otherwise in running the site) –  Mad Scientist Jul 30 at 9:36
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@Mad Scientist Still, the chances that this type of theoretical question will be answered on Biostars are higher. The answered bioinformatics questions on this site are usually more practical approaches/use cases/... I did not imply the question is off-topic otherwise I would have flagged it as such. I just wanted to be helpful. –  skymninge Jul 30 at 9:43
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All bioinformatics questions are on-topic. Just that if someone requires technical help then biostars has more people who can help. –  WYSIWYG Jul 30 at 12:00
    
having said that, this question seems quite broad to me. More details need to be provided. –  WYSIWYG Jul 30 at 12:01

1 Answer 1

My Vote goes to Mafft(insi) as it have ~86% accuracy and results in ~1.2 hour. Though fastest will be kalign takes only ~3 minutes to finish with an accuracy of 74.3%.

For testing:

For each of the 218 reference alignments in the benchmark, we applied eight alignment programs, resulting in a total of 1744 automatically constructed MSAs. The overall quality of these automatic alignments was measured using the Column Score (CS) described in Methods.

enter image description here FIGURE 1: Overall alignment performance for each of the MSA programs tested.

(A) Overall Accuracy

(B) Total run time for constructing all alignments (a log10 scale is used for display purposes).

doi:10.1371/journal.pone.0018093.g003

Compared Tools

Source and Photo Credits:

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

PS: This is from an old paper of 2011. If you want the new statistics you can always test on your own, by the process described in the source paper.

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Personally, I always use muscle + gblocks for proteins. Does the job well enough, IMO. –  5heikki Jul 30 at 12:19
    
@5heikki: I agree. Muscle is actually good. –  Devashish Das Jul 30 at 12:26
    
Always Clustalx FTW! –  caseyr547 Jul 30 at 21:20
    
I dont think any of them has a parallelization option. I think parallelization is possible for pairwise distance calculation step atleast. –  WYSIWYG Jul 31 at 8:11

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