Tools for Multiple Alignments
If you have problems or comments...
Search for sequence similarities in databases
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
- 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).
- 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).
(Unix, Mac, PC, VMS).
- ClustalX (IGBMC , EBI) (ClustalW graphical interface)
(Unix, Mac, PC, VMS).
- Multiple alignment by randomized iterative strategy (Gotoh's RIW/DNR methods)
- BlastAlign (Linux, Mac OS X).
- Kalign (source code available under GNU license)
Multiple alignment editors
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)
(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.
(For Mac and Unix).
Colour multiple alignment editor for secondary structure prediction.
Colour multiple alignment editor.
Particularly useful for manipulating protein coding DNA/RNA sequences.
Interactive extendable and scriptable editor for large protein alignments.
Open source "Microsoft Excel"-based bioinformatics tool for protein sequence alignment and analysis.
(Web-based multiple alignment viewer)
Pretty printing, shading, logos, etc.
Databases of alignments
- PIRALN section of the Protein Alignment Database ( PIR)
Homologous vertebrate genes (alignments and phylogenetic trees).
hierarchical classification of all SWISS-PROT proteins.
Molecular Sequence Megaclassification.
- PROTAL2DNA (Pasteur, Paris) Back-translate a protein alignment into a DNA alignment
(San Francisco, USA) Performs the Evolutionary Trace along with other
phylogenomic analysis - it combines alignment, phylogeny and protein
- Mumsa (Stockholm, Sweden) A program to assess the quality of multiple sequence alignments
See also ...
Index of services in molecular biology
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