List of alignment visualization software: Difference between revisions

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Line 1: {{Short description\|none}} This page is a subsection of the [[list of sequence alignment software]]. Line 10 ⟶ 11: == Alignment viewers, editors == {\| class="wikitable sortable" \|- ! Name Line 19 ⟶ 20: ! Format support ! [[Software license\|License]] !Can run on Browser !Operating Platforms ! Link \|- Line 28 ⟶ 31: \| [[FASTA format\|FASTA]], [[Clustal]] \| {{free}}, [[GNU General Public License\|GPL]] 3 \|No \|Linux Terminal \| {{Official website\|https://github.com/mpdunne/alan}} \|- Line 37 ⟶ 42: \| GenBank, EMBL, [[FASTA format\|FASTA]], [[PHYLIP]] \| {{free}}, [[GNU General Public License\|GPL]] \|No \|GNU Emacs \| {{Official website\|www.red-bean.com/ale}} \|- \| AliView ~~2018~~2025 \| {{no}} \| {{yes\|MUSCLE integrated; other programs such as MAFFT can be defined}} Line 46 ⟶ 53: \| [[FASTA format\|FASTA]], [[FASTQ]], [[PHYLIP]], [[Nexus file\|Nexus]], MSF, [[Clustal]] \| {{free}}, [[GNU General Public License\|GPL]] 3 \|? \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|www.ormbunkar.se/aliview}} \|- \| alv \| {{no}} \| {{no}} \| {{no}} \| Console-based (no GUI), yet with colors. Coding DNA is coloured by codon. \| [[FASTA format\|FASTA]], [[PHYLIP]], [[Nexus file\|Nexus]], [[Clustal]], [[Stockholm format\|Stockholm]] \| {{free}}, [[GNU General Public License\|GPL]] 3 \| No \|Cross-platform \| {{Official website\|https://pypi.org/project/alv/}}, see also {{GitHub\|https://github.com/arvestad/alv}} \|- \| [[ARB_Project\|arb]] \| {{yes\|structure editable, show bond in helix sequence regions, 2D molecule viewer}} \| {{yes\|MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference)}} \| {{yes\|arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayes}} \| Edits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA. Custom column highlighting (e.g. by conservation profiles). Designs, matches and [http://www.arb-home.de/images/arb_secedit_large.png visualizes probes]. \| [[FASTA format\|FASTA]], [[GenBank]], [[EMBL]], [[Newick format\|Newick]] \| {{proprietary}}, [[freeware]], [http://vc.arb-home.de/readonly/trunk/arb_LICENSE.txt arb license], open modifiable source \| No \|Linux, Mac OS (homebrew) \| {{Official website\|http://www.arb-home.de/}} \|- \| Base-By-Base Line 55 ⟶ 90: \| Genbank, [[FASTA format\|FASTA]], EMBEL, [[Clustal]], base-by-base files \| {{proprietary}}, [[freeware]], must register \|? \|? \| {{Official website\|athena.bioc.uvic.ca/virology-ca-tools/base-by-base}} \|- Line 64 ⟶ 101: \| Genbank, [[FASTA format\|FASTA]], [[PHYLIP]] 3.2 and 4, NBRF-PIR \| {{proprietary}}, [[freeware]] \|No \|Windows (95/98/NT/2000/XP) \| {{Official website\|www.mbio.ncsu.edu/BioEdit/bioedit.html}} \|- Line 73 ⟶ 112: \| Genbank, [[FASTA format\|FASTA]] \| {{proprietary}}, [[Commercial software\|commercial]] \|? \|? \| {{Official website\|www.applied-maths.com/bionumerics/bionumerics.htm}} \|- Line 82 ⟶ 123: \| [[FASTA]], [[FASTQ]], [[Clustal]], [[SAM_(file_format)\|SAM]], [[Variant_Call_Format\|VCF]] and more \| {{free}}, [[GNU General Public License\|GPL]] 3 \|No \|Vim, Less, GEdit, & Sublime \| {{Official website\|https://bioSyntax.org}} \|- Line 91 ⟶ 134: \| MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by [[Clustal]]W \| {{free}}, [[public ___domain]] \|No \|MSDOS, VMS \| {{Official website\|ch.embnet.org/software/BOX_form.html}} \|- Line 100 ⟶ 145: \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], [[PHYLIP]], [[Protein Information Resource\|PIR]], PRINTS \| {{proprietary}}, [[freeware]] \|No \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|aig.cs.man.ac.uk/research/utopia/cinema/cinema.php}} \|- Line 109 ⟶ 156: \| many \| {{proprietary}}, [[freeware]]. More options available in commercial versions. \|No \|? \| {{Official website\|www.clcbio.com}} \|- \| CIAlign \| {{no}} \| {{no}} \| {{no}} \| Alignment visualisation as publication-ready images, alignment cleaning. \| [[FASTA format\|FASTA]] \| {{free}}, [[MIT License\|MIT]] \| No \| Linux, Windows, MacOS \| {{Official website\|https://github.com/KatyBrown/CIAlign}} [[doi:10.7717/peerj.12983\|Publication]] \|- \| [[Clustal]]X viewer Line 118 ⟶ 179: \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], [[PHYLIP]] \| {{proprietary}}, [[freeware]] for academic use \|No \|Command line \| {{Official website\|www.clustal.org}} \|- \| [[CodonCode Aligner]] \| {{no \| no, but can read, add & show structure annotations}} \| {{yes\|[[Clustal]], MUSCLE, various built-in algorithms}} \| {{yes\| Yes}} \| Multi- and pairwise alignments, assembly, sequence translation, editing, trimming, mutation detection, restriction analysis, cloning, primer design, dotplot, much more \| ABI, SCF, [[FASTA format\|FASTA]], FASTQ, [[Nexus file\|Nexus]]/PAUP or [[PHYLIP]], Sam, Bam, .dna, EMBL, GenBank, BLAST, GFF \| {{proprietary}}, [[Commercial software\|commercial]], Viewer is [[Freeware]] \|No \|Mac OS, Windows \| {{Official website\|www.codoncode.com/aligner}} \|- \| Cylindrical Alignment App Line 127 ⟶ 201: \| BLAST XML, proprietary XML, GFF3, [[Clustal]]W, INSDSet, user expandable with [[XSLT]] \| {{free}}, [[Common Development and Distribution License\|CDDL 1.]] Available for dual licensing. \|? \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|sourceforge.net/projects/cylindrical-alignment-app}} \|- Line 136 ⟶ 212: \| BLAST XML, proprietary XML, GFF3, [[Clustal]]W, INSDSet, user expandable with [[XSLT]] \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|sourceforge.net/projects/cyl-viewer}} \|- Line 145 ⟶ 223: \| FASTA, FASTQ, GenBank \| {{free}}, [[GNU General Public License\|GPL]] \|No \|Mac OS, Windows \| {{Official website\|decipher.cee.wisc.edu/Download.html}} \|- Line 154 ⟶ 234: \| BSML, EMBL, GB, HELM, [[Clustal]], [[FASTA]], GDE, [[Protein Data Bank (file format)\|PDB]], SEQ, SPT, ... \| {{proprietary}}, [[Commercial software\|commercial]], Viewer is [[Freeware]] \|? \|Linux, Windows \| {{Official website\|accelrys.com/products/discovery-studio/visualization-download.php}} \|- Line 162 ⟶ 244: \| Can compute several population genetics statistics, reconstruct haplotypes with PHASE \| [[FASTA]], [[Nexus file\|Nexus]], MEGA, [[PHYLIP]] \| {{proprietary}}, [[Commercial software\|commercial]], [[freeware]] for ~~noncomercial~~noncommercial use \|? \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|www.ub.es/dnasp}} \|- Line 172 ⟶ 256: \| ABI, DNA Multi-Seq, [[FASTA format\|FASTA]], GCG Pileup, GenBank, Phred \| {{proprietary}}, [[Commercial software\|commercial]], academic licenses available \|? \|Mac OS, Windows \| {{Official website\|www.dnastar.com/t-sub-solutions-molecular-biology-sequence-alignment.aspx}} \|- Line 181 ⟶ 267: \| {{dunno}} \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|archive.debian.net/lenny/biomode}} \|- Line 190 ⟶ 278: \| FASTA \| {{proprietary}}, [[Commercial software\|commercial]], [[freeware]] for noncommercial use \|? \|? \| {{Official website\|flakbio.com}} \|- Line 199 ⟶ 289: \| many \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|www.nrbsc.org/gfx/genedoc}} [http://www.nrbsc.org/gfx/genedoc/gdpaf.htm table of features] \|- Line 208 ⟶ 300: \| >40 file formats imported and exported \| {{proprietary}}, [[Commercial software\|commercial]]; personal, floating \|? \|Cross-platform - Mac, Windows, Linux \| {{Official website\|www.geneious.com}} \|- Line 217 ⟶ 311: \| BAM, [[FASTA format\|FASTA]], PSL \| {{free}}, [[Common Public License\|CPL]] \|? \|Cross-platform - Mac, Windows, Linux \| {{Official website\|igb.bioviz.org}} \|- Line 226 ⟶ 322: \| FASTA \| {{proprietary}}, free use \|Yes \|Browser \| {{Official website\|itol.embl.de}} \|- Line 235 ⟶ 333: \| [[Clustal]]W, MSF, [[PHYLIP]], [[Protein Information Resource\|PIR]], GDE, Nexus \| {{proprietary}}, [[freeware]] \|? ~~\| {{Bad link 10 Nov 2017\|www.ivistmsa.com}}~~ \|? \| www.ivistmsa.com \|- \| [[Jalview]] \| {{yes\|Secondary structure prediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ ~~JNET~~JPred 4]}} \| {{yes\|[[Clustal#Clustal_Omega\|Clustal O]], [[Clustal]], GLprobs, MSAprobs, [[MUSCLE (alignment software)\|MUSCLE]], [[MAFFT]], Probcons, TCoffee, via web services}} \| {{yes\|[[UPGMA]], [[Neighbor joining\|NJ]]}} \| Sequences and features retrieved from user-configurable and publicly registered servers, e.g. [[European_Molecular_Biology_Laboratory\|EMBL]], [[European_Bioinformatics_Institute\|EBI]], [[Protein_Data_Bank\|PDB]], [[Pfam]], [[Rfam]], [[UniProt]] Accession retrieval. Structure/model data retrieval from [[Protein_Data_Bank\|PDB]] and 3D-Beacons including [[Protein_Data_Bank\|PDBe]], [[AlphaFold#Protein_Structure_Database\|AlphaFold DB]], [[Swiss-model\|SWISS-MODEL]]. ~~\| Sequences and features from arbitrary and publicly registered [[Distributed Annotation System\|DAS]] servers, PFAM, PDB, EMBL, Uniprot Accession retrieval.~~ \| [[FASTA format\|FASTA]], [[~~PFAM format\|PFAM~~Pfam]], MSF, [[Clustal]], ~~[[BLC format\|~~BLC]], [[Protein Information Resource\|PIR]], [[Stockholm format\|Stockholm]], [[Variant_Call_Format\|VCF]], AMSA, BioJSON, Clustal, [[European_Nucleotide_Archive#EMBL-Bank_format\|ENA]], [[GenBank]], [[General_feature_format\|GFF2]], [[General_feature_format\|GFF3]], JnetFile, [[PHYLIP]], [[Pileup_format\|PileUp]], RNAML, [[Crystallographic_Information_File\|CIF]], [[Crystallographic_Information_File\|mmCIF]], [[Protein_Data_Bank_(file_format)\|PDB]]. \| {{free}}, [[GNU General Public License\|GPL]] \| ~~{{Official website\|~~[https://www.jalview.org}}/jalview-js/ JalviewJS] (Javascript) \|Cross-platform - macOS, Linux, Windows, other with Java Virtual Machine. \| {{Official website\|https://www.jalview.org/}} \|- \| Jevtrace Line 253 ⟶ 355: \| [[FASTA format\|FASTA]], MSF, [[Clustal]], [[PHYLIP]], [[Newick format\|Newick]], [[Protein Data Bank (file format)\|PDB]] \| {{proprietary}}, [[Commercial software\|commercial]], [[freeware]] for academic use \|? \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|compbio.berkeley.edu/people/marcin/jevtrace}} [http://compbio.berkeley.edu/people/marcin/jevtrace/jevtracev3.12_manual.pdf manual] \|- Line 262 ⟶ 368: \| An array of JavaScript objects \| {{free}}, [[GNU General Public License\|GPL]] 2 \|Yes \|Browser \| {{Official website\|www.bioinf.org.uk/software/jsav}} \|- \|Lucid Align\| Lucid Align \| {{no}} \| {{no}} \| {{no}} \|BAM, FASTQ, FASTA\| Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data \|BAM, FASTQ, FASTA \| {{proprietary}}, [[Commercial software\|commercial]], [[freeware]] for academic use \|No \|Mac OS \|{{Official website\|https://www.lucidalign.com}} \|- \| Maestro Line 271 ⟶ 390: \| [[Clustal]], [[FASTA format\|FASTA]] [[Protein Data Bank\|PDB]] \| {{proprietary}}, [[freeware]] for academic use \|? \|? \| {{Official website\|www.schrodinger.com/products/14/12}} \|- Line 280 ⟶ 401: \| FASTA, [[Clustal]], Nexus, MEGA, etc. \| {{proprietary}}, [[freeware]], must register \|? \|? \| {{Official website\|www.megasoftware.net}} \|- Line 289 ⟶ 412: \| [[Clustal]], [[FASTA format\|FASTA]], [[Protein Data Bank\|PDB]], EMBL, GCG, GCG_MSF, Genbank, [[PHYLIP]], [[Protein Information Resource\|PIR]], raw_seq \| {{proprietary}} \|? \|? \| {{Official website\|www.chemcomp.com/MOE-Molecular_Operating_Environment.htm}} \|- Line 298 ⟶ 423: \| FASTA \| {{free}}, [[Creative Commons license\|Creative Commons]] Attribution NonCommercial [[Share-alike]] \|? \|? \| {{Official website\|msareveal.org}} \|- Line 307 ⟶ 434: \| FASTA, PDB, ALN, [[PHYLIP]], NEXUS \| {{proprietary}}, [[freeware]], but VMD is free for noncommercial use only \|? \|? \| {{Official website\|www.scs.illinois.edu/schulten/multiseq}} \|- Line 316 ⟶ 445: \| BLAST search, [[FASTA format\|FASTA]] search, [[Clustal]], HSSP, [[FASTA format\|FASTA]], [[Protein Information Resource\|PIR]], MSF \| {{free}}, [[GNU General Public License\|GPL]] \|No ~~\| {{Official website\|bio-mview.sourceforge.net}}~~ \|Cross-platform - Mac OS, Linux, Windows \| {{Official website\|desmid.github.io/mview}} \|- \| PFAAT Line 325 ⟶ 456: \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], PFAAT \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|pfaat.sourceforge.net}} \|- Line 334 ⟶ 467: \| [[Stockholm format\|Stockholm]] \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257}} \|- Line 343 ⟶ 478: \| [[FASTA format\|FASTA]], RnaML \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|bioinformatics.org/S2S}} \|- Line 351 ⟶ 488: \| Dot-plot, [[vim (text editor)\|vim]]-like editing keys \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], [[PHYLIP]], [[MASE format\|MASE]] \| {{~~proprietary~~free}}, [[~~freeware~~GNU General Public License\|GPL]] 3 \|? \| Linux, Mac OS, Windows \| {{Official website\|pbil.univ-lyon1.fr/software/seaview.html}} \|- Line 358 ⟶ 497: \| {{yes\|[[MUSCLE (alignment software)\|MUSCLE]], [[MAFFT]]}} \| {{yes\|[[UPGMA]], [[Neighbor joining\|NJ]], ML (Physher)}} \| Manual alignment, tree visualisation~~; runs on Mac [[OS X]]~~ \| [[Nexus file\|Nexus]], [[Clustal]], [[FASTA format\|FASTA]], [[PHYLIP]], [[MEGA, Molecular Evolutionary Genetics Analysis\|MEGA]], [[Stockholm format\|Stockholm]], NBRF/[[Protein Information Resource\|PIR]], GDE flat \| {{free}}, [[GNU General Public License\|GPL]] \|? \|Mac OS X \| {{Official website\|github.com/4ment/seqotron}} [https://www.ncbi.nlm.nih.gov/pubmed/26887850 publication] \|- Line 370 ⟶ 511: \| Accession number, GI number, PDB ID, [[FASTA]], drag-drop from external [[URL]] from within the user interface \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|www.sequilab.org}} \|- \| ~~SeqPop~~SeqPup \| {{no}} \| {{dunno}} Line 379 ⟶ 522: \| {{dunno}} \| {{proprietary}}, [[freeware]] \|? ~~\| {{Official website\|iubio.bio.indiana.edu/soft/molbio/seqpup/java}}~~ \|? \| {{Official website\|iubioarchive.bio.net/soft/molbio/seqpup/java/}} \|- \| Sequlator Line 388 ⟶ 533: \| MSF \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|sequlator.com}} \|- Line 397 ⟶ 544: \| FASTA, newick \| {{free}}, [[Apache License\|Apache]] 2.0 \|Yes ~~\| {{Official website\|github.com/yeastrc/snipviz}}, [https://www.ncbi.nlm.nih.gov/pubmed/?term=25056180 publication]~~ \|Browsers \| {{Official website\|github.com/yeastrc/snipviz}}, [https://pubmed.ncbi.nlm.nih.gov/25056180/ publication] \|- \| Strap Line 406 ⟶ 555: \| MSF, [[Stockholm format\|Stockholm]], [[Clustal]]W, [[Nexus file\|Nexus]], [[FASTA]], [[Protein Data Bank (file format)\|PDB]], Embl, [[GenBank]], [[hssp]], [[Pfam]] \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|3d-alignment.eu}} \|- Line 415 ⟶ 566: \| [[ACE (genomic file format)\|ACE]], AFG, MAQ, SOAP2, [[BAM format\|SAM]], [[BAM format\|BAM]], [[FASTA format\|FASTA]], [[FASTQ format\|FASTQ]], [[General feature format\|GFF3]] \| {{free}}, [[BSD licenses\|BSD]] 2-clause \|? \|? \| {{Official website\|ics.hutton.ac.uk/tablet}} \|- Line 424 ⟶ 577: \| [[FASTA format\|FASTA]], [[FASTQ format\|FASTQ]], [[GenBank]], [[EMBL]], ABIF, SCF, [[Clustal]]W, [[Stockholm format\|Stockholm]], Newick, [[Protein Data Bank\|PDB]], MSF, GFF \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|ugene.unipro.ru}} \|- Line 433 ⟶ 588: \| [[Clustal]], [[FASTA format\|FASTA]] \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|bioinformatics.burnham.org/liwz/vissa}} \|- Line 442 ⟶ 599: \| [[FASTA format\|FASTA]], [[FASTQ format\|FASTQ]], [[GenBank]] \| {{free}}, [[GNU General Public License\|GPL]] 3 \|? \|? \| {{Official website\|https://github.com/mengqvist/DNApy}} \|- Line 448 ⟶ 607: \| {{yes\|By sequence or mixed sequence and structure}} \| {{yes\|Includes [[Archaeopteryx (evolutionary tree visualization and analysis)\|Archaeopteryx]]}} \| ~~Running in modern web browsers of desktop PCs, tablets (iOS, Android, MS-Mobile).~~ [[Distributed Annotation System\|DAS]] and user defined annotations. Scriptable. Export to HTML, Word, [[Jalview]]. \| Many \| {{free}}, [[GNU General Public License\|GPL]] \|Yes \|iOS, Android, MS-Mobile, Browsers \| {{Official website\|www.bioinformatics.org/strap/aa}} \|} ~~Some useful discussions on sequence alignment editors/viewers can be found here:~~ * http://lists.open-bio.org/pipermail/emboss/2008-July/003324.html ==See also== Line 463 ⟶ 622: {{DEFAULTSORT:Alignment visualization software}} [[Category:~~Bioinformatics~~Lists of bioinformatics software]] [[Category:Visualization ~~(graphic)~~software\|Software]] ~~[[Category:Lists of software]]~~