“List of alignment visualization software”的意思、由来-开放百科全书

词条

List of alignment visualization software

释义

Alignment viewers, editors
See also

This page is a subsection of the list of sequence alignment software.

Multiple alignment visualization tools typically serve four purposes:

Aid general understanding of large-scale DNA or protein alignments
Visualize alignments for figures and publication
Manually edit and curate automatically generated alignments
Analysis in depth

The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is necessary because algorithms for both multiple sequence alignment and structural alignment use 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 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	Structure prediction tools integrated	Can align sequences	Can calculate phylogenetic trees	Other features	Format support	License	Can run on Browser	Operating Platforms	Link
Alan	{{no}}	{{no}}	{{no}}	Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding	FASTA, Clustal	{{free}}, GPL 3	No	Linux Terminal	https://github.com/mpdunne/alan}}
Ale (emacs plugin)	{{no}}	{{yes}}	{{no}}	{{no}}	GenBank, EMBL, FASTA, PHYLIP	{{free}}, GPL	No	GNU Emacs	www.red-bean.com/ale}}
AliView 2018	{{no}}	MUSCLE integrated; other programs such as MAFFT can be defined}}	External programs such as FastTree can be called from within}}	Fast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design.	FASTA, FASTQ, PHYLIP, Nexus, MSF, Clustal	{{free}}, GPL 3	?	Cross-platform -Mac OS, Linux, Windows	www.ormbunkar.se/aliview}}
alv	{{no}}	{{no}}	{{no}}	Console-based (no GUI), yet with colors. Coding DNA is coloured by codon.	FASTA, PHYLIP, Nexus, Clustal, Stockholm	{{free}}, GPL 3	No	Cross-platform	https://pypi.org/project/alv/}}, see also {{GitHub\|https://github.com/arvestad/alv}}
Base-By-Base	{{no}}	MUSCLE}}	UPGMA, NJ, complete and single linkages, WPMGA}}	Visual summary, percent identity tables, some integrated advanced analysis tools	Genbank, FASTA, EMBEL, Clustal, base-by-base files	{{proprietary}}, freeware, must register	?	?	athena.bioc.uvic.ca/virology-ca-tools/base-by-base}}
BioEdit	{{no}}	ClustalW}}	Rudimentary, can read PHYLIP}}	Plasmid drawing, ABI chromatograms,	Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR	{{proprietary}}, freeware	No	Windows (95/98/NT/2000/XP)	www.mbio.ncsu.edu/BioEdit/bioedit.html}}
BioNumerics	{{no}}	{{yes}}	{{yes}}	{{dunno}}	Genbank, FASTA	{{proprietary}}, commercial	?	?	www.applied-maths.com/bionumerics/bionumerics.htm}}
bioSyntax	{{no}}	{{no}}	{{no}}	Native syntax highlighting support for Vim, less, gedit and Sublime	FASTA, FASTQ, Clustal, SAM, VCF and more	{{free}}, GPL 3	No	Vim, Less, GEdit, & Sublime	https://bioSyntax.org}}
BoxShade	{{no}}	{{no}}	{{no}}	Specifically for multiple alignments	MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalW	{{free}}, public domain	No	MSDOS, VMS	ch.embnet.org/software/BOX_form.html}}
CINEMA	{{no}}, but can read-show 2D structure annotations	ClustalW}}	{{no}}	Dotplot, 6 frame translation, Blast	Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS	{{proprietary}}, freeware	No	Cross-platform -Mac OS, Linux, Windows	aig.cs.man.ac.uk/research/utopia/cinema/cinema.php}}
CLC viewer (free version)	Commercial version only}}	Clustal, MUSCLE, T-Coffee, MAFFT, Kalign, various}}	UPGMA, NJ}}	Workflows, blast-genbank search	many	{{proprietary}}, freeware. More options available in commercial versions.	?	?	www.clcbio.com}}
ClustalX viewer	{{no}}	ClustalW}}	NJ}}	Alignment quality analysis	Nexus, MSF, Clustal, FASTA, PHYLIP	{{proprietary}}, freeware for academic use	No	Command line	www.clustal.org}}
Cylindrical Alignment App	{{no}}	{{no}}	{{no}}	3D, animation, drilldown, legend selection	BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT	{{free}}, CDDL 1. Available for dual licensing.	?	Cross-platform -Mac OS, Linux, Windows	sourceforge.net/projects/cylindrical-alignment-app}}
Cylindrical BLAST Viewer	{{no}}	{{no}}	{{no}}	3D, animation, drilldown, legend selection	BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT	{{free}}, GPL	?	?	sourceforge.net/projects/cyl-viewer}}
DECIPHER	{{yes}}	{{yes}}	UPGMA, NJ, ML}}	Primer-Probe design, Chimera finding	FASTA, FASTQ, GenBank	{{free}}, GPL	No	Mac OS, Windows	decipher.cee.wisc.edu/Download.html}}
Discovery Studio	{{yes}}	Align123, ClustalW, S-ALIGN}}	UPGMA, NJ, with bootstrap and best tree}}	Visualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, more	BSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT, ...	{{proprietary}}, commercial, Viewer is Freeware	?	Linux, Windows	accelrys.com/products/discovery-studio/visualization-download.php}}
DnaSP	{{dunno}}	{{dunno}}	{{dunno}}	Can compute several population genetics statistics, reconstruct haplotypes with PHASE	FASTA, Nexus, MEGA, PHYLIP	{{proprietary}}, commercial, freeware for noncomercial use	?	Cross-platform -Mac OS, Linux, Windows	www.ub.es/dnasp}}
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, translation	ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred	{{proprietary}}, commercial, academic licenses available	?	Mac OS, Windows	www.dnastar.com/t-sub-solutions-molecular-biology-sequence-alignment.aspx}}
emacs - biomode	{{dunno}}	{{dunno}}	{{dunno}}	{{dunno}}	{{dunno}}	{{free}}, GPL	?	?	archive.debian.net/lenny/biomode}}
FLAK	{{no}}	Can perform fuzzy whole genome alignment}}	{{no}}	Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options	FASTA	{{proprietary}}, commercial, freeware for noncommercial use	?	?	flakbio.com}}
Genedoc	{{no}}, but can read-show annotations	Pairwise}}	{{no}}, but can read-show annotations	gel simulation, stats, multiple views, simple	many	{{proprietary}}, freeware	?	?	www.nrbsc.org/gfx/genedoc}} 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, much more	>40 file formats imported and exported	{{proprietary}}, commercial; personal, floating	?	Cross-platform - Mac, Windows, Linux	www.geneious.com}}
Integrated Genome Browser (IGB)	{{no}}	{{no}}	{{no}}	Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers	BAM, FASTA, PSL	{{free}}, CPL	?	Cross-platform - Mac, Windows, Linux	igb.bioviz.org}}
interactive Tree Of Life (iTOL)	{{no}}	{{no}}	{{dunno}}	Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments.	FASTA	{{proprietary}}, free use	Yes	Browser	itol.embl.de}}
IVisTMSA	{{no}}	Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment}}	Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx}}	Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator	ClustalW, MSF, PHYLIP, PIR, GDE, Nexus	{{proprietary}}, freeware	?	?	www.ivistmsa.com}}
Jalview	Secondary structure 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, Uniprot Accession retrieval.	FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm	{{free}}, GPL	Applet	Cross-platform -Mac OS, Linux, Windows	www.jalview.org}}
Jevtrace	Integrated with structure viewer WebMol}}	{{no}}	{{no}}	A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive [https://www.ncbi.nlm.nih.gov/pubmed/8609628 Evolutionary Trace] and other phylogeny inspired analysis.	FASTA, MSF, Clustal, PHYLIP, Newick, PDB	{{proprietary}}, commercial, freeware for academic use	?	Cross-platform -Mac OS, Linux, Windows	compbio.berkeley.edu/people/marcin/jevtrace}} manual
JSAV	{{no}}	{{no}}	{{no}}	A JavaScript component allowing integrating an alignment viewer into web pages	An array of JavaScript objects	{{free}}, GPL 2	Yes	Browser	www.bioinf.org.uk/software/jsav}}
Maestro	{{yes}}	ClustalX}}	{{yes}}	Mapping from sequence to 3D structure, structure-sequence editing-modeling	Clustal, FASTA PDB	{{proprietary}}, freeware for academic use	?	?	www.schrodinger.com/products/14/12}}
MEGA	{{no}}	Native ClustalW}}	UPGMA, NJ, ME, MP, with bootstrap and confidence test}}	Extended support to phylogenetics analysis	FASTA, Clustal, Nexus, MEGA, etc.	{{proprietary}}, freeware, must register	?	?	www.megasoftware.net}}
Molecular Operating Environment (MOE)	{{yes}}	{{yes}}	{{yes}}	Part of an extensive collection of applications for sequence to structure, including homology modelling; 3D visualisation, etc.	Clustal, FASTA, PDB, EMBL, GCG, GCG_MSF, Genbank, PHYLIP, PIR, raw_seq	{{proprietary}}	?	?	www.chemcomp.com/MOE-Molecular_Operating_Environment.htm}}
MSAReveal.org	{{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}}, Creative Commons Attribution NonCommercial Share-alike	?	?	msareveal.org}}
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, PHYLIP, NEXUS	{{proprietary}}, freeware, but VMD is free for noncommercial use only	?	?	www.scs.illinois.edu/schulten/multiseq}}
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	{{free}}, GPL	No	Cross-platform - Mac OS, Linux, Windows	desmid.github.io/mview}}
PFAAT	{{no}}, but can display 3D structures	ClustalW}}	NJ}}	Manual annotation, conservation scores	Nexus, MSF, Clustal, FASTA, PFAAT	{{proprietary}}, freeware	?	?	pfaat.sourceforge.net}}
Ralee (emacs plugin for RNA al. editing)	{{dunno}}	RNA structure}}	{{dunno}}	{{dunno}}	Stockholm	{{free}}, GPL	?	?	bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257}}
S2S RNA editor	2D structure}}	Rnalign}}	{{no}}	Base-base interactions, 2D-3D viewer	FASTA, RnaML	{{proprietary}}, freeware	?	?	bioinformatics.org/S2S}}
Seaview	{{no}}	local MUSCLE-ClustalW}}	Parsimony, distance methods, PhyML}}	Dot-plot, vim-like editing keys	Nexus, MSF, Clustal, FASTA, PHYLIP, MASE	{{proprietary}}, freeware	?	?	pbil.univ-lyon1.fr/software/seaview.html}}
Seqotron	{{no}}	MUSCLE, MAFFT}}	UPGMA, NJ, ML (Physher)}}	Manual alignment, tree visualisation	Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat	{{free}}, GPL	?	Mac OS X	github.com/4ment/seqotron}} [https://www.ncbi.nlm.nih.gov/pubmed/26887850 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, drag-drop from external URL from within the user interface	{{proprietary}}, freeware	?	?	www.sequilab.org}}
SeqPop	{{no}}	{{dunno}}	{{dunno}}	{{dunno}}	{{dunno}}	{{proprietary}}, freeware	?	?	iubio.bio.indiana.edu/soft/molbio/seqpup/java}}
Sequlator	{{no}}	Pairwise alignment}}	{{no}}	easy alignment editing	MSF	{{proprietary}}, freeware	?	?	sequlator.com}}
SnipViz	{{no}}	{{no}}	{{no}} (but can display them)	Pure Javascript and HTML; suitable to integrate in websites	FASTA, newick	{{free}}, Apache 2.0	Yes	Browsers	github.com/yeastrc/snipviz}}, [https://www.ncbi.nlm.nih.gov/pubmed/?term=25056180 publication]
Strap	Jnet, NNPREDICT, Coiled coil, 16 different TM-helix}}	15 different methods}}	NJ}}	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	{{free}}, GPL	?	?	3d-alignment.eu}}
Tablet	{{no}}	{{no}}	{{no}}	High-performance graphical viewer for viewing next generation sequence assemblies and alignments.	ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3	{{free}}, BSD 2-clause	?	?	ics.hutton.ac.uk/tablet}}
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	{{free}}, GPL	?	?	ugene.unipro.ru}}
VISSA sequence-structure viewer	DSSP secondary structure}}	ClustalX}}	{{no}}	Mapping from sequence to 3D structure	Clustal, FASTA	{{proprietary}}, freeware	?	?	bioinformatics.burnham.org/liwz/vissa}}
DNApy	{{no}}	MUSCLE}}	{{no}}	Editing of GenBank files, plasmid drawing, ABI chromatograms,	FASTA, FASTQ, GenBank	{{free}}, GPL 3	?	?	https://github.com/mengqvist/DNApy}}
Alignment Annotator	{{yes}}	By sequence or mixed sequence and structure}}	Includes Archaeopteryx}}	DAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview.	Many	{{free}}, GPL	Yes	iOS, Android, MS-Mobile, Browsers	www.bioinformatics.org/strap/aa}}

Alignment viewers, editors

See also