Multiple alignment visualization tools typically serve three purposes:
- Visualization of alignments for figures and publication.
- Manual editing and curation of automatically generated alignments.
- In depth analysis
The first is a natural consequence of the fact that most computational representations of alignments and their annotation are not human readable and best portrayed in the familiar seuqence row and alignment column format, of which examples are widespread in the literature. The second is a necessity because Multiple sequence alignment algorithms utilise heuristics which do not always perform perfectly. The third is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools in order to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence (e.g. comparative modelling).
Alignment Viewers/Editors
| Name | Integrated with Struct. Prediction Tools | Can Align Sequences | Can Calculate Phylogenetic Trees | Other Features | Formats Supported | License | Link | |
|---|---|---|---|---|---|---|---|---|
| DnaSP | can compute several population genetics statistics, reconstruct haplotypes with PHASE | FASTA, NEXUS, Mega, PHYLIP | Freeware | link | ||||
| Strap | Jnet, NNPREDICT, Coiled coil, 16 different TM-helix | Fifteen different Methods | Neighbor-joining | Dot-plot, Structure-neighbors, 3D-superposition, Blast-search, Mutation/SNP analysis, Sequence features, Biojava-interface | MSF, Stockholm, Clustalw, Nexus, FASTA, PDB, Embl, GenBank, hssp, Pfam | GPL | link | |
| Seaview | No | local Muscle/Clustalw | No | Dot-plot, vim-like editing keys | NEXUS, MSF, Clustal, FASTA, PHYLIP, MASE | link | ||
| Jalview 2 | Secondary Struct. Prediction via JNET | Clustal, Muscle, MAFFT via web services | UPGMA, NJ | sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL and Uniprot Accession retrieval. | FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm | GPL | link | |
| CLC viewer (Free version) | only in commercial version | Clustal, Muscle, T-Coffee, MAFFT, kalign, various | UPGMA, NJ | workflows, blast/genbank search | many | Freeware. More options available in commercial versions. | link, table of features | |
| UGENE | No | MUSCLE | No | many | FASTA, GenBank, EMBL, ABIF, SCF, CLUSTALW, Stockholm, Newick, PDB | GPL | link | |
| Mega | No | Native ClustalW | UPGMA, NJ, ME, MP, with bootstrap and confidence test | extended support to phylogenetics analysis | FASTA, Clustal, Nexus, Mega, etc.. | Freeware, registration requested | link, table of features | |
| Genedoc | No, but can read/show annotations | Pairwise | No, but can read/show annotations | gel simulation, stats, multiple views, simple | many | Free | link table of features | |
| SeqPop | No | Free | link | |||||
| BioEdit | No | ClustalW | rudimentary, can read phylip | plasmid drawing, ABI chromatograms, | Genbank, Fasta, Phylip 3.2, Phylip 4, NBRF/PIR | Free | link | |
| Ale (emacs plugin) | No | Yes | No | No | GenBank, EMBL, Fast-A, and Phylip | GPL | link | |
| Ralee (emacs plugin for RNA al. editing) | RNA structure | Stockholm | GPL | link | ||||
| emacs - biomode | link |
Some useful discussions on sequence alignment editors/viewers can be found here: