Tools for Multiple Alignments

Search for sequence similarities in databases

• WU-BLAST at ISREC (Lausanne, Switzerland)
• BLAST2 Search at EMBL (Heidelberg, Germany) Performs multiple alignment on homologous sequences detected by BLAST.
• FASTA at EBI (Hinxton, UK)
• Smith-Waterman search at EBI (Hinxton, UK)
• BCM search launcher (Houston, USA)
• GeneStream at CRBM (Montpellier, France)
• BLAST search at PBIL (Lyon, France) Possibility to select BLAST output results by taxa or keyword.

Web Sites for Pairwise Alignments

• LFASTA - Local alignment tool at PBIL (Lyon, France)
• SIM4 - align cDNA and genomic DNA at PBIL (Lyon, France)
• WISE - align protein and genomic DNA at Pasteur (Paris, France)
• SIM - Alignment Tool at ExPASy (Geneva, Switzerland)
• BLAST two sequences at NCBI (Bethesda, USA)
• LALIGN at CRBM (Montpellier, France)
• SIM, GAP, NAP, LAP (Michigan Tech. Univ., USA)
• JAligner: open source Java implementation of the Smith-Waterman algorithm (Alexandria, Egypt)

Web Sites for Multiple Alignments

• MAFFT (Tokyo, Japan)
• Muscle at EBI (Hinxton, UK).
• ClustalW2 at EBI (Hinxton, UK). Display and edit alignments with JalView.
• ClustalW, Multalin at PBIL (Lyon, France). Colored alignments and secondary structure predictions.
• ClustalW, MAP, PIMA at BCM (Houston, USA)
• MSA, ClustalW, ctree at IBC (St Louis, USA)
• Multalin at INRA (Toulouse, France). Colored alignments.
• ClustalW, DCA, DIALIGN2 at Pasteur (Paris, France)
• ClustalW at EMBL (Heidelberg, Germany). Performs multiple alignment on homologous sequences detected by BLAST.
• ClustalW at DDBJ (Mishima, Japan)
• MAP (Michigan Tech. Univ., USA)
• ProbModel at CBRG (Zurich, Switzerland)
• DIALIGN2 at BiBiServ (Bielefeld, Germany)
• DCA at BiBiServ (Bielefeld, Germany)
• ITERALIGN (Stanford, USA)
• T-COFFEE (Lausanne, Switzerland)
• MATCH-BOX (Namur, Belgium)
• BLOCK Maker at FHCRC (Washington, USA)
• MEME at SDSC (San Diego, USA)
• MEME at Pasteur (Paris, France)
• PIMA II at BMERC (Boston, USA)
• MAVID at UCB (Berkeley, USA)
• ClustalW, MAFFT, PRRN at GenomeNet (Kyoto, Japan)
• BlastAlign at BioAfrica (Pretoria, South Africa)
• Kalign at the Karolinska Institute (Stockholm, Sweden)

Software for Multiple Alignments

• MUSCLE (Linux, Unix, Windows XP, Mac OS X).
• MAFFT (Linux, Unix, Windows XP, Mac OS X).
• ClustalW (Unix, Mac, PC, VMS).
• ClustalX (IGBMC , EBI) (ClustalW graphical interface) (Unix, Mac, PC, VMS).
• Multalin
• MSA (Unix).
• DIALIGN (Unix).
• DCA (Unix).
• Multiple alignment by randomized iterative strategy (Gotoh's RIW/DNR methods) (Unix).
• MACAW (Mac, PC).
• T-Coffee (Unix).
• BlastAlign (Linux, Mac OS X).
• Kalign (source code available under GNU license)

Multiple alignment editors

• Jalview Java multiple alignment editor.(Java)
  Colour by amino acid physico-chemical property, similarity to consensus sequence, hydrophobicity or secondary structure. Gaps can be inserted/deleted using the mouse. UPGMA and NJ trees calculated and drawn based on percent identity distances. And much more ...
• CINEMA 2.1 Colour INteractive Editor for Multiple Alignments (Java).
  Alignments may be loaded from the PRINTS fingerprint database. And much more ...
• JavaShade Java multiple alignment editor. (Java)
  
• SEAVIEW (For Mac, PC, Unix and Linux computers).
  A colour graphical interface to manually edit the alignment, and also to run dot-plot or Clustal W programs to locally improve the alignment. And much more ... Can be used in in combination with PHYLO_WIN for phylogenetic analyses.
• MPSA (For Mac and Unix).
  Colour multiple alignment editor for secondary structure prediction.
• Belvu (For Unix).
  Colour multiple alignment editor.
• Se-Al (For Mac).
  Particularly useful for manipulating protein coding DNA/RNA sequences.
• DCSE (For Unix).
• STRAP (Java)
  Interactive extendable and scriptable editor for large protein alignments.
• GoCore (Microsoft Excel)
  Open source "Microsoft Excel"-based bioinformatics tool for protein sequence alignment and analysis.
• Kalignvu (Web-based multiple alignment viewer)

Pretty printing, shading, logos, etc.

• BOXSHADE (Lausanne, Switzerland) Highlight conserved residues, save in various formats for article preparation.
• WebLogo (Cambridge, UK)
• Mview (London, UK)
• AMAS (Dundee, UK)
• TEXshade: A LaTeX package for setting nucleotide and peptide alignments (Tuebingen, Deutschland)

Databases of alignments

• PIRALN section of the Protein Alignment Database ( PIR)
• HOVERGEN Homologous vertebrate genes (alignments and phylogenetic trees).
• PROTOMAP hierarchical classification of all SWISS-PROT proteins.
• Megaclass Molecular Sequence Megaclassification.

• Prodom
• PRINTS
• DOMO
• PFAM
• BLOCKS

• Ribosomal Database Project (Michigan State University, USA)
  rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences
• The rRNA WWW server (University of Antwerp, Belgium)
  alignments of LSU and SSU rRNA sequences (and more ...)
• HIV sequence database (LANL, USA)
  Annotated and aligned HIV sequences

Miscellaneous

• PROTAL2DNA (Pasteur, Paris) Back-translate a protein alignment into a DNA alignment
• JEvTrace (San Francisco, USA) Performs the Evolutionary Trace along with other phylogenomic analysis - it combines alignment, phylogeny and protein structure.
• Mumsa (Stockholm, Sweden) A program to assess the quality of multiple sequence alignments

See also ...

• The BioCatalog (Hinxton, UK) Catalog of software for molecular biology.
• VSNS BioComputing Division Multiple Alignment Resource Page (Bielefeld, Germany) List of WWW resources for multiple alignments.

Index of services in molecular biology

• BioNetbook Institut Pasteur (Paris, France)
• Bioinformatics links (Lyngby, Denmark)
• Infobiogen Deambulum (Paris, France)
• Baylor College of Medicine (Houston, USA)
• USGS Index of Biology servers (Reston, USA)
• Bioinformatics software on the Web (Baltimore, USA)
• Amos Bairoch's WWW links page (Geneva, Switzerland)