http://probcons.stanford.edu/

PROBCONS is an efficient protein multiple sequence alignment program,

which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

http://lagan.stanford.edu/lagan_web/index.shtml

CHAOS
CHAOS is a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome. It uses both exact matching and degenerate seeds, and is able to find homology in the presence of gaps.
LAGAN
LAGAN is our highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors;
Multi-LAGAN
Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric.
Shuffle-LAGAN
Shuffle-LAGAN is a novel glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework. It uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny.

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

(download and install multiple alignment programs on your local computer)

• 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

Protein families.

• 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.

Protein domains.

• Prodom
• PRINTS
• DOMO
• PFAM
• BLOCKS

RNA/DNA.

• 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)