Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).

By contrast, Multiple Sequence Alignment (MSA) is the alignment of three or more biological sequences of similar length. From the output of MSA applications, homology can be inferred and the evolutionary relationship between the sequences studied.

Global Alignment

Global alignment tools create an end-to-end alignment of the sequences to be aligned.

Needle (EMBOSS)

EMBOSS Needle creates an optimal global alignment of two sequences using the Needleman-Wunsch algorithm.

Launch Needle

Stretcher (EMBOSS)

EMBOSS Stretcher uses a modification of the Needleman-Wunsch algorithm that allows larger sequences to be globally aligned.

Launch Stretcher

Local Alignment

Local alignment tools find one, or more, alignments describing the most similar region(s) within the sequences to be aligned. They are can align protein and nucleotide sequences.

Water (EMBOSS)

EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancements) to calculate the local alignment of two sequences.

Launch Water

Matcher (EMBOSS)

EMBOSS Matcher identifies local similarities between two sequences using a rigorous algorithm based on the LALIGN application.

Launch Matcher


LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or DNA sequences.


Genomic Alignment

Genomic alignment tools concentrate on DNA (or to DNA) alignments while accounting for characteristics present in genomic data.


GeneWise compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

Launch GeneWise

The tools described on this page are provided using The EMBL-EBI search and sequence analysis tools APIs in 2019

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