List of alignment visualization software
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 of an alignment: perhaps to explore its 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 | Secundary Struct. Prediction via JNET | Clustal, Muscle via web services | UPGMA, NJ | features from arbitrary DAS servers | FASTA, PFAM, MSF, Clustal, BLC, PIR | 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: