This page is a subsection of List of sequence alignment software.
Multiple alignment visualization tools typically serve four purposes:
The rest of this article is focused on just multiple global alignments of homologous proteins. The first two are 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 sequence row and alignment column format, of which examples are widespread in the literature. The third is a necessity because both Multiple sequence alignment and Structural alignment algorithms utilise heuristics which do not always perform perfectly. The fourth 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).
| Name | Integrated with Struct. Prediction Tools | Can Align Sequences | Can Calculate Phylogenetic Trees | Other Features | Formats Supported | License | Link | |
|---|---|---|---|---|---|---|---|---|
| Ale (emacs plugin) | No | Yes | No | No | GenBank, EMBL, Fast-A, and Phylip | GPL | link | |
| BioEdit | No | ClustalW | rudimentary, can read phylip | plasmid drawing, ABI chromatograms, | Genbank, Fasta, Phylip 3.2, Phylip 4, NBRF/PIR | Free | link | |
| CINEMA | NO, but can read/show 2D structure annotations | ClustalW | No | Dotplot, 6 frame translation, Blast | Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS | Free | 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 | |
| ClustalX viewer | No | Clustalw | Neighbor-joining | Alignment quality analysis | Nexus, MSF, Clustal, FASTA, PHYLIP | Free for academic users | link | |
| Cylindrical BLAST Viewer | No | No | No | 3D, Animation, Drilldown, Legend Selection | BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT | GPL | link | |
| DnaSP | can compute several population genetics statistics, reconstruct haplotypes with PHASE | FASTA, Nexus, Mega, PHYLIP | Freeware | link | ||||
| emacs - biomode | link | |||||||
| 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 | |
| Geneious Pro | Yes - powered by EMBOSS tools | Clustal, Muscle, MAUVE, profile, translation | UPGMA, NJ, PhyML, MrBayes plugin, PAUP* plugin | Whole genome assembly, restriction analysis, cloning, primer design, dotplot and much more | >40 file formats imported and exported | Geneious Basic (freeware) Geneious Pro (commercial with student and academic discounts) | link | |
| Integrated Genome Browser (IGB) | No | No | No | sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers | BAM, FASTA, PSL | CPL | link | |
| Jalview 2 | Secondary Struct. Prediction via JNET | Clustal, Muscle, MAFFT, Probcons, TCoffee 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 | |
| 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 | |
| Multiseq (vmd plugin) | No, but can display and align 3D structures | ClustaLW, MaFFT, Stamp (Strutural) | Percent identity, Clustal, MaFFT, Structural | Scripting via Tcl, mapping from sequence to 3D structure | FASTA, PDB, ALN, PHYLYP, NEXUS | Free, but VMD is free only for noncommercial use | link | |
| MView | No | No | No | stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns | BLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSF | GPL | link | |
| PFAAT | NO, but can display 3D structures | ClustalW | Neighbor-joining | Manual annotation, conservation scores | Nexus, MSF, Clustal, FASTA, PFAAT | Free | link | |
| Ralee (emacs plugin for RNA al. editing) | RNA structure | Stockholm | GPL | link | ||||
| S2S RNA editor | 2D structure | Rnalign | No | base-base interactions,2D,3D viewer | FASTA, RnaML | Free | link | |
| Seaview | No | local Muscle/Clustalw | Parcimony, distance methods, PhyML | Dot-plot, vim-like editing keys | Nexus, MSF, Clustal, FASTA, PHYLIP, MASE | link | ||
| Sequilab | Yes | Yes | No | Link alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbars | Accession number, GI number, PDB ID, FASTA, DragNdrop from external URL from within the user interface | Freeware | link | |
| SeqPop | No | Free | 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 | |
| UGENE | Yes | MUSCLE, KAlign | Yes | many | FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, CLUSTALW, Stockholm, Newick, PDB, MSF, GFF | GPL | link | |
| VISSA sequence/structure viewer | DSSP secondary structure | ClustalX | No | Mapping from sequence to 3D structure | Clustal, FASTA | Free | link |
Some useful discussions on sequence alignment editors/viewers can be found here: