Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied.
By contrast, Pairwise Sequence Alignment tools are used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences.
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Clustal Omega
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New MSA tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments. Suitable for medium-large alignments.
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ClustalW2
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Popular MSA tool that uses tree-based progressive alignments. Suitable for medium alignments.
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DbClustal
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Create a Multiple Sequence Alignment from a protein BLAST result using the DbClustal program.
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Kalign
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Very fast MSA tool that concentrates on local regions. Suitable for large alignments.
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MAFFT
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MSA tool that uses Fast Fourier Transforms. Suitable for medium-large alignments.
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MUSCLE
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Accurate MSA tool, especially good with proteins. Suitable for medium alignments.
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MView
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Transform a Sequence Similarity Search result into a Multiple Sequence Alignment or reformat a Multiple Sequence Alignment using the MView program.
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T-Coffee
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Consistency-based MSA tool that attempts to mitigate the pitfalls of progressive alignment methods. Suitable for small alignments.
- WebPRANK
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The EBI has a new phylogeny-aware multiple sequence alignment program which makes use of evolutionary information to help place insertions and deletions.
Try it out at WebPRANK.
The tools described on this page are provided using our new bioinformatics analysis tools framework. If you have any feedback or encounter any issues please let us know via EMBL-EBI support.