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 45 ⟶ 46: \| {{Official website\|www.red-bean.com/ale}} \|- \| AliView ~~2018~~2025 \| {{no}} \| {{yes\|MUSCLE integrated; other programs such as MAFFT can be defined}} Line 70 ⟶ 71: \|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.~~jalview~~arb-home.~~org~~de/}}▼ \|- \| Base-By-Base Line 144 ⟶ 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 158 ⟶ 182: \|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 209 ⟶ 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 Line 300 ⟶ 335: \|? \|? \| ~~{{Bad link 10 Nov 2017\|~~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]] \|[https://www.jalview.org/jalview-js/ JalviewJS] (Javascript) ~~\|Applet~~ \|Cross-platform -~~Mac~~ OSmacOS, Linux, Windows, other with Java Virtual Machine. \| {{Official website\|https://www.jalview.org/}} ▲Windows ▲\| {{Official website\|www.jalview.org}} \|- \| Jevtrace Line 338 ⟶ 371: \|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 444 ⟶ 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 471 ⟶ 515: \| {{Official website\|www.sequilab.org}} \|- \| ~~SeqPop~~SeqPup \| {{no}} \| {{dunno}} Line 480 ⟶ 524: \|? \|? \| {{Official website\|~~iubio~~iubioarchive.bio.~~indiana.edu~~net/soft/molbio/seqpup/java/}} \|- \| Sequlator Line 502 ⟶ 546: \|Yes \|Browsers \| {{Official website\|github.com/yeastrc/snipviz}}, [https://~~www~~pubmed.ncbi.nlm.nih.gov/~~pubmed/?term=~~25056180/ publication] \|- \| Strap Line 571 ⟶ 615: \| {{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 581 ⟶ 622: {{DEFAULTSORT:Alignment visualization software}} [[Category:~~Bioinformatics~~Lists of bioinformatics software]] [[Category:Visualization ~~(graphic)~~software\|Software]] ~~[[Category:Lists of software]]~~