List of alignment visualization software

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This page is a subsection of List of sequence alignment software.

Multiple alignment visualization tools typically serve four purposes:

  • General comprehension of large-scale DNA or protein alignments
  • Visualization of alignments for figures and publication.
  • Manual editing and curation of automatically generated alignments.
  • In depth analysis

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).

Alignment viewers/editors[edit]

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, Fasta, and Phylip GPL link
AliView 2016 No Muscle is integrated. Other programs such as MAFFT can be defined. External programs such as FastTree can be called from within Fast, very easy navigation through unlimited mouse wheel zoom in/out feature. Handles unlimited file size alignments. Degenerate primer design. FASTA, PHYLIP, Nexus, MSF and Clustal GPL3 link
Base-By-Base No Muscle UPGMA, NJ, Complete Linkage, Single Linkage, WPMGA Visual summary, percent identity tables, some integrated advanced analysis tools Genbank, Fasta, EMBEL, Clustal, Base-by-base files Free, registration required link
BioEdit No ClustalW rudimentary, can read phylip plasmid drawing, ABI chromatograms, Genbank, Fasta, Phylip 3.2, Phylip 4, NBRF/PIR Free link
BioNumerics No Yes Yes Genbank, Fasta Commercial link
BoxShade No No No Specifically for multiple alignments MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq). ALN format as written by CLUSTALW. Public domain 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
DECIPHER Yes Yes UPGMA, NJ, ML Primer/Probe design, Chimera finding FASTA, FASTQ, GenBank GPL link
Discovery Studio Yes Align123, ClustalW, S-ALIGN UPGMA, NJ, with bootstrap and best tree Visualizer supports 2D and 3D structure and sequence. Full featured version has comprehensive functionality for Protein, nucleotides and more. BSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT,... Viewer is free for everyone link
DnaSP can compute several population genetics statistics, reconstruct haplotypes with PHASE FASTA, Nexus, Mega, PHYLIP Freeware link
DNASTAR Lasergene Molecular Biology Suite Yes Yes Yes Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, and translation. ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred Commercial, Academic licenses available link
emacs - biomode link
FLAK No Yes. Can perform a fuzzy whole genome alignment No. Very fast and highly customisable. Visualisation is WYSIWYG with filtering and fuzzy options. FASTA Free for noncommercial use 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 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 Personal and Floating 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
interactive Tree Of Life (iTOL) No No Phylogenetic tree viewer/annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to the alignments. FASTA Free link manual
IVistMSA No Clustal Omega, ClustalW2, MAFFT, MUSCLE and BioJava have been integrated for constructing alignment Tree calculation tool calculates a phylogenetic tree using BioJava API and permits the user to draw the tree using Archaeopteryx IVisTMSA is a software package of seven interactive visual tools for multiple sequence alignments. Major focus is on manipulating large alignments. It includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator ClustalW, MSF, Phylip, PIR, GDE, and Nexus Free 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
JEvTrace No but integrated with structure viewer WebMol No No A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis. FASTA, MSF, Clustal, PHYLIP, Newick, PDB Free for academic use link manual
JSAV No No No A JavaScript component allowing integration of an alignment viewer into web pages. An array of JavaScript objects GPL2 link
Maestro Yes ClustalX Yes Mapping from sequence to 3D structure, structure/sequence editing/modeling Clustal, FASTA PDB Free for Academics 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 No No No Optional coloring. Touching AA shows 3-letter code and sequence number. Touching consensus shows AA frequencies in that column. Counts and percentages of aromatics, charged, gaps. FASTA Free, open source, Creative Commons Attribution NonCommercial ShareAlike link features
Multiseq (vmd plugin) No, but can display and align 3D structures ClustalW, MAFFT, Stamp (Structural) 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 Parsimony, distance methods, PhyML Dot-plot, vim-like editing keys Nexus, MSF, Clustal, FASTA, PHYLIP, MASE link
Seqotron No MUSCLE, MAFFT UPGMA, NJ, ML (Physher) Manual alignment, tree visualisation. Runs on Mac OS X. Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat GPL link publication
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
Sequlator No Pairwise alignment No easy alignment editing MSF Free link
SnipViz No No No (but can display them) Pure Javascript and HTML. Suitable for integration into web sites. FASTA, newick Apache 2.0 link publication
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
Tablet No No No High-performance graphical viewer for viewing next generation sequence assemblies and alignments. ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, and GFF3 Open source, (c)James Hutton Institute link
UGENE Yes MUSCLE, KAlign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith-Waterman algorithm 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
DNApy No MUSCLE No Editing of GenBank files, plasmid drawing, ABI chromatograms, FASTA, FASTQ, GenBank GPL3 link
Alignment Annotator Yes By sequence or mixed sequence and structure Includes Archaeopteryx Running in modern web browsers of desktop PCs + tablets (iOS, Android, MS-Mobile). Distributed Annotation System and user defined annotations. Scriptable. Export to HTML, Word and Jalview. Many GPL link

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

See also[edit]