List of alignment visualization software: Difference between revisions

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{{Short description|none}}

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

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== Alignment viewers, editors ==

{| class="wikitable sortable"

|-

! Name

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| {{Official website|www.red-bean.com/ale}}

|-

| AliView 20182025

| {{no}}

| {{yes|MUSCLE integrated; other programs such as MAFFT can be defined}}

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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.jalviewarb-home.orgde/}}

|-

| Base-By-Base

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| 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

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|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

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| Can compute several population genetics statistics, reconstruct haplotypes with PHASE

| [[FASTA]], [[Nexus file|Nexus]], MEGA, [[PHYLIP]]

| {{proprietary}}, [[Commercial software|commercial]], [[freeware]] for noncomercialnoncommercial use

|?

|Cross-platform -Mac OS, Linux, Windows

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|?

|?

| {{Bad link 10 Nov 2017|www.ivistmsa.com}}

|-

| [[Jalview]]

| {{yes|Secondary structure prediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ JNETJPred 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|PFAMPfam]], 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

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|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

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| BLAST search, [[FASTA format|FASTA]] search, [[Clustal]], HSSP, [[FASTA format|FASTA]], [[Protein Information Resource|PIR]], MSF

| {{free}}, [[GNU General Public License|GPL]]

|?No

|Cross-platform - Mac OS, Linux, Windows

|?

| {{Official website|bio-mviewdesmid.sourceforgegithub.netio/mview}}

|-

| PFAAT

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| Dot-plot, [[vim (text editor)|vim]]-like editing keys

| [[Nexus file|Nexus]], MSF, [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP]], [[MASE format|MASE]]

| {{proprietaryfree}}, [[freewareGNU General Public License|GPL]] 3

|?

|?

| Linux, Mac OS, Windows

| {{Official website|pbil.univ-lyon1.fr/software/seaview.html}}

|-

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| {{Official website|www.sequilab.org}}

|-

| SeqPopSeqPup

| {{no}}

| {{dunno}}

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|?

|?

| {{Official website|iubioiubioarchive.bio.indiana.edunet/soft/molbio/seqpup/java/}}

|-

| Sequlator

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|Yes

|Browsers

| {{Official website|github.com/yeastrc/snipviz}}, [https://wwwpubmed.ncbi.nlm.nih.gov/pubmed/?term=25056180/ publication]

|-

| Strap

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| {{free}}, [[GNU General Public License|GPL]]

|Yes

|iOS, AndriodAndroid, 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==

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{{DEFAULTSORT:Alignment visualization software}}

[[Category:BioinformaticsLists of bioinformatics software]]

[[Category:Visualization (graphic)software|Software]]

[[Category:Lists of software]]