Revision as of 11:46, 4 February 2018 edit 213.114.53.61 (talk) No edit summary ← Previous edit		Revision as of 18:49, 7 March 2018 edit undo 46.208.6.78 (talk) Added columns for 'Can run on browser' and 'Operating platforms' and populated as many rows as possible with data provided on each tool's website. Tag: Visual edit Next edit →
Line 19: ! Format support ! [[Software license\|License]] !Can run on Browser !Operating Platforms ! Link \|- Line 28 ⟶ 30: \| [[FASTA format\|FASTA]], [[Clustal]] \| {{free}}, [[GNU General Public License\|GPL]] 3 \|No \|Linux Terminal \| {{Official website\|https://github.com/mpdunne/alan}} \|- Line 37 ⟶ 41: \| GenBank, EMBL, [[FASTA format\|FASTA]], [[PHYLIP]] \| {{free}}, [[GNU General Public License\|GPL]] \|No \|GNU Emacs \| {{Official website\|www.red-bean.com/ale}} \|- Line 46 ⟶ 52: \| [[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}} \|- Line 55 ⟶ 67: \| 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 ⟶ 78: \| 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 ⟶ 89: \| Genbank, [[FASTA format\|FASTA]] \| {{proprietary}}, [[Commercial software\|commercial]] \|? \|? \| {{Official website\|www.applied-maths.com/bionumerics/bionumerics.htm}} \|- Line 82 ⟶ 100: \| [[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 ⟶ 111: \| 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 ⟶ 122: \| [[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 ⟶ 133: \| many \| {{proprietary}}, [[freeware]]. More options available in commercial versions. \|? \|? \| {{Official website\|www.clcbio.com}} \|- Line 118 ⟶ 144: \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], [[PHYLIP]] \| {{proprietary}}, [[freeware]] for academic use \|No \|Command line \| {{Official website\|www.clustal.org}} \|- Line 127 ⟶ 155: \| 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 ⟶ 166: \| 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 ⟶ 177: \| FASTA, FASTQ, GenBank \| {{free}}, [[GNU General Public License\|GPL]] \|No \|Mac OS, Windows \| {{Official website\|decipher.cee.wisc.edu/Download.html}} \|- Line 154 ⟶ 188: \| 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 163 ⟶ 199: \| [[FASTA]], [[Nexus file\|Nexus]], MEGA, [[PHYLIP]] \| {{proprietary}}, [[Commercial software\|commercial]], [[freeware]] for noncomercial use \|? \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|www.ub.es/dnasp}} \|- Line 172 ⟶ 210: \| 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 ⟶ 221: \| {{dunno}} \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|archive.debian.net/lenny/biomode}} \|- Line 190 ⟶ 232: \| FASTA \| {{proprietary}}, [[Commercial software\|commercial]], [[freeware]] for noncommercial use \|? \|? \| {{Official website\|flakbio.com}} \|- Line 199 ⟶ 243: \| many \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|www.nrbsc.org/gfx/genedoc}} [http://www.nrbsc.org/gfx/genedoc/gdpaf.htm table of features] \|- Line 208 ⟶ 254: \| >40 file formats imported and exported \| {{proprietary}}, [[Commercial software\|commercial]]; personal, floating \|? \|Cross-platform - Mac, Windows, Linux \| {{Official website\|www.geneious.com}} \|- Line 217 ⟶ 265: \| BAM, [[FASTA format\|FASTA]], PSL \| {{free}}, [[Common Public License\|CPL]] \|? \|Cross-platform - Mac, Windows, Linux \| {{Official website\|igb.bioviz.org}} \|- Line 226 ⟶ 276: \| FASTA \| {{proprietary}}, free use \|Yes \|Browser \| {{Official website\|itol.embl.de}} \|- Line 235 ⟶ 287: \| [[Clustal]]W, MSF, [[PHYLIP]], [[Protein Information Resource\|PIR]], GDE, Nexus \| {{proprietary}}, [[freeware]] \|? \|? \| {{Bad link 10 Nov 2017\|www.ivistmsa.com}} \|- Line 244 ⟶ 298: \| [[FASTA format\|FASTA]], [[PFAM format\|PFAM]], MSF, [[Clustal]], [[BLC format\|BLC]], [[Protein Information Resource\|PIR]], [[Stockholm format\|Stockholm]] \| {{free}}, [[GNU General Public License\|GPL]] \|Applet \|Cross-platform -Mac OS, Linux, Windows \| {{Official website\|www.jalview.org}} \|- Line 253 ⟶ 311: \| [[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 ⟶ 324: \| An array of JavaScript objects \| {{free}}, [[GNU General Public License\|GPL]] 2 \|Yes \|Browser \| {{Official website\|www.bioinf.org.uk/software/jsav}} \|- Line 271 ⟶ 335: \| [[Clustal]], [[FASTA format\|FASTA]] [[Protein Data Bank\|PDB]] \| {{proprietary}}, [[freeware]] for academic use \|? \|? \| {{Official website\|www.schrodinger.com/products/14/12}} \|- Line 280 ⟶ 346: \| FASTA, [[Clustal]], Nexus, MEGA, etc. \| {{proprietary}}, [[freeware]], must register \|? \|? \| {{Official website\|www.megasoftware.net}} \|- Line 289 ⟶ 357: \| [[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 ⟶ 368: \| FASTA \| {{free}}, [[Creative Commons license\|Creative Commons]] Attribution NonCommercial [[Share-alike]] \|? \|? \| {{Official website\|msareveal.org}} \|- Line 307 ⟶ 379: \| 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 ⟶ 390: \| BLAST search, [[FASTA format\|FASTA]] search, [[Clustal]], HSSP, [[FASTA format\|FASTA]], [[Protein Information Resource\|PIR]], MSF \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|bio-mview.sourceforge.net}} \|- Line 325 ⟶ 401: \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], PFAAT \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|pfaat.sourceforge.net}} \|- Line 334 ⟶ 412: \| [[Stockholm format\|Stockholm]] \| {{free}}, [[GNU General Public License\|GPL]] \|? \|? \| {{Official website\|bioinformatics.oxfordjournals.org/cgi/content/full/21/2/257}} \|- Line 343 ⟶ 423: \| [[FASTA format\|FASTA]], RnaML \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|bioinformatics.org/S2S}} \|- Line 352 ⟶ 434: \| [[Nexus file\|Nexus]], MSF, [[Clustal]], [[FASTA format\|FASTA]], [[PHYLIP]], [[MASE format\|MASE]] \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|pbil.univ-lyon1.fr/software/seaview.html}} \|- Line 358 ⟶ 442: \| {{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 ⟶ 456: \| Accession number, GI number, PDB ID, [[FASTA]], drag-drop from external [[URL]] from within the user interface \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|www.sequilab.org}} \|- Line 379 ⟶ 467: \| {{dunno}} \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|iubio.bio.indiana.edu/soft/molbio/seqpup/java}} \|- Line 388 ⟶ 478: \| MSF \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|sequlator.com}} \|- Line 397 ⟶ 489: \| FASTA, newick \| {{free}}, [[Apache License\|Apache]] 2.0 \|Yes \|Browsers \| {{Official website\|github.com/yeastrc/snipviz}}, [https://www.ncbi.nlm.nih.gov/pubmed/?term=25056180 publication] \|- Line 406 ⟶ 500: \| 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 ⟶ 511: \| [[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 ⟶ 522: \| [[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 ⟶ 533: \| [[Clustal]], [[FASTA format\|FASTA]] \| {{proprietary}}, [[freeware]] \|? \|? \| {{Official website\|bioinformatics.burnham.org/liwz/vissa}} \|- Line 442 ⟶ 544: \| [[FASTA format\|FASTA]], [[FASTQ format\|FASTQ]], [[GenBank]] \| {{free}}, [[GNU General Public License\|GPL]] 3 \|? \|? \| {{Official website\|https://github.com/mengqvist/DNApy}} \|- Line 448 ⟶ 552: \| {{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, Andriod, MS-Mobile, Browsers \| {{Official website\|www.bioinformatics.org/strap/aa}} \|}

List of alignment visualization software: Difference between revisions