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Sequence alignments tools
NCBI Blast
The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between nucleotides and protein sequences. Align two or more sequences or find similarities between your sequence of interests and entire genomes.
ENSEMBL Blast
The ENSEMBL Alignment Search Tools are as good as the NCBI tools for finding regions of local similarity between nucleotides and protein sequences.
EMBOSS Needle
If you are only interested in pairwise alignment, try out the EMBL-EBI EMBOSS Needle