Template:wikipedia list This page is a subsection of List of sequence alignment 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

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 sequence row and alignment column format, of which examples are widespread in the literature. The second is a necessity because both Multiple sequence alignment and Structural 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 Edit

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
ClustalX viewer No Clustalw Neighbor-joining Alignment quality analysis NEXUS, MSF, Clustal, FASTA, PHYLIP Free for academic users link
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
VISSA sequence/structure viewer DSSP secondary structure ClustalX No Mapping from sequence to 3D structure Clustal, FASTA Free 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 Yes MUSCLE, KAlign Yes many FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, CLUSTALW, Stockholm, Newick, PDB, MSF, GFF 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
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
PFAAT NO, but can display 3D structures ClustalW Neighbor-joining Manual annotation, conservation scores NEXUS, MSF, Clustal, FASTA, PFAAT Free link
S2S RNA editor 2D structure Rnalign No base-base interactions,2D,3D viewer FASTA, RnaML Free link

Some useful discussions on sequence alignment editors/viewers can be found here:

See alsoEdit

[[Category:Visualization (graphic)|Software

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