Sequence Alignment Resources

Database Search

NCBI BLAST Server - a popular server for database searches in the US.

EBI BLAST - BLAST database searches at the European Bioinformatics Institute.

Sequence Alignment Servers

Sequence Analysis tools at the EBI - a collection of tools for DNA sequence analysis, including tools for pairwise and multiple sequence alignment.

  • ClustalW2 - align sequences with ClustalW.
  • MAFFT - fast multiple sequence alignments with MAFFT.
  • MUSCLE - accurate & fast sequence alignments.
  • T-Coffee - multiple sequence alignment program that can combine results from other alignment programs.

Pairwise alignments at Michigan Tech.

Multiple sequence alignment for protein and DNA sequences at Michigan Tech.

MAFFT alignment server in Japan, with download links.

Kalign Swedish server for aligning multiple sequences.

Web Directories

Wikipedia's list of sequence alignment software.

List of alignment tools at the University of Lyon.

ExPASy Life Science Directory - a database-centric list of life science resources.