Multiple Sequence Alignment Software Mac

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Reads and writes several alignment formats, translates nucleotide to protein sequences and can colour nucleotide sequences by codon (very helpful for in-frame alignment). Also has in-built.

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were im. Question: Multiple Alignment Software. 6.4 years ago. Can you recommend a free online multiple alignment software for aligning large number of sequences.

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Mauve development began at the University of Wisconsin-Madison with a team including Aaron Darling, Bob Mau, and Nicole Perna. Several others have contributed development to aspects of the Mauve software in the time since.

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.

Multiple Sequence Alignment Software Machine


Alignment viewers, editors[edit]

NameStructure prediction tools integratedCan align sequencesCan calculate phylogenetic treesOther featuresFormat supportLicenseCan run on BrowserOperating PlatformsLink
AlanNoNoNoAllows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwardingFASTA, ClustalFree, GPL 3NoLinux TerminalOfficial website
Ale (emacs plugin)NoYesNoNoGenBank, EMBL, FASTA, PHYLIPFree, GPLNoGNU EmacsOfficial website
AliView 2019NoMUSCLE integrated; other programs such as MAFFT can be definedExternal programs such as FastTree can be called from withinFast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design.FASTA, FASTQ, PHYLIP, Nexus, MSF, ClustalFree, GPL 3?Cross-platform -Mac OS,



Official website
alvNoNoNoConsole-based (no GUI), yet with colors. Coding DNA is coloured by codon.FASTA, PHYLIP, Nexus, Clustal, StockholmFree, GPL 3NoCross-platformOfficial website, see also alv on GitHub
arbstructure editable, show bond in helix sequence regions, 2D molecule viewerMUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference)arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayesEdits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA. Custom column highlighting (e.g. by conservation profiles). Designs, matches and visualizes probes.FASTA, GenBank, EMBL, NewickProprietary, freeware, arb license, open modifiable sourceNoLinux, Mac OS (homebrew)Official website
Base-By-BaseNoMUSCLEUPGMA, NJ, complete and single linkages, WPMGAVisual summary, percent identity tables, some integrated advanced analysis toolsGenbank, FASTA, EMBEL, Clustal, base-by-base filesProprietary, freeware, must register??Official website
BioEditNoClustalWRudimentary, can read PHYLIPPlasmid drawing, ABI chromatograms,Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIRProprietary, freewareNoWindows (95/98/NT/2000/XP)Official website
BioNumericsNoYesYes?Genbank, FASTAProprietary, commercial??Official website
bioSyntaxNoNoNoNative syntax highlighting support for Vim, less, gedit and SublimeFASTA, FASTQ, Clustal, SAM, VCF and moreFree, GPL 3NoVim, Less, GEdit, & SublimeOfficial website
BoxShadeNoNoNoSpecifically for multiple alignmentsMSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalWFree, public domainNoMSDOS, VMSOfficial website
CINEMANo, but can read-show 2D structure annotationsClustalWNoDotplot, 6 frame translation, BlastNexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTSProprietary, freewareNoCross-platform -Mac OS, Linux, WindowsOfficial website
CLC viewer (free version)Commercial version onlyClustal, MUSCLE, T-Coffee, MAFFT, Kalign, variousUPGMA, NJWorkflows, blast-genbank searchmanyProprietary, freeware. More options available in commercial versions.No?Official website
ClustalX viewerNoClustalWNJAlignment quality analysisNexus, MSF, Clustal, FASTA, PHYLIPProprietary, freeware for academic useNoCommand lineOfficial website
Cylindrical Alignment AppNoNoNo3D, animation, drilldown, legend selectionBLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLTFree, CDDL 1. Available for dual licensing.?Cross-platform -Mac OS, Linux, WindowsOfficial website
Cylindrical BLAST ViewerNoNoNo3D, animation, drilldown, legend selectionBLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLTFree, GPL??Official website
DECIPHERYesYesUPGMA, NJ, MLPrimer-Probe design, Chimera findingFASTA, FASTQ, GenBankFree, GPLNoMac OS, WindowsOfficial website
Discovery StudioYesAlign123, ClustalW, S-ALIGNUPGMA, NJ, with bootstrap and best treeVisualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, moreBSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT, ...Proprietary, commercial, Viewer is Freeware?Linux, WindowsOfficial website
DnaSP???Can compute several population genetics statistics, reconstruct haplotypes with PHASEFASTA, Nexus, MEGA, PHYLIPProprietary, commercial, freeware for noncomercial use?Cross-platform -Mac OS, Linux, WindowsOfficial website
DNASTAR Lasergene Molecular Biology SuiteYesYesYesAlign 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, translationABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, PhredProprietary, commercial, academic licenses available?Mac OS, WindowsOfficial website
emacs - biomode?????Free, GPL??Official website
FLAKNoCan perform fuzzy whole genome alignmentNoVery fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy optionsFASTAProprietary, commercial, freeware for noncommercial use??Official website
GenedocNo, but can read-show annotationsPairwiseNo, but can read-show annotationsgel simulation, stats, multiple views, simplemanyProprietary, freeware??Official websitetable of features
GeneiousYes - powered by EMBOSS toolsClustal, MUSCLE, MAUVE, profile, translationUPGMA, NJ, PhyML, MrBayes plugin, PAUP* pluginWhole genome assembly, restriction analysis, cloning, primer design, dotplot, much more>40 file formats imported and exportedProprietary, commercial; personal, floating?Cross-platform - Mac, Windows, LinuxOfficial website
Integrated Genome Browser (IGB)NoNoNoSequences and features from files, URLs, and arbitrary DAS and QuickLoad serversBAM, FASTA, PSLFree, CPL?Cross-platform - Mac, Windows, LinuxOfficial website
interactive Tree Of Life (iTOL)NoNo?Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments.FASTAProprietary, free useYesBrowserOfficial website
IVisTMSANoClustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignmentTree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using ArchaeopteryxSoftware 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 calculatorClustalW, MSF, PHYLIP, PIR, GDE, NexusProprietary, freeware??
JalviewSecondary structure prediction via JNETClustal, MUSCLE, MAFFT, Probcons, TCoffee via web servicesUPGMA, NJSequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL, Uniprot Accession retrieval.FASTA, PFAM, MSF, Clustal, BLC, PIR, StockholmFree, GPLAppletCross-platform -Mac OS, Linux,


Official website
JevtraceIntegrated with structure viewer WebMolNoNoA multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis.FASTA, MSF, Clustal, PHYLIP, Newick, PDBProprietary, commercial, freeware for academic use?Cross-platform -Mac OS, Linux,


Official websitemanual
JSAVNoNoNoA JavaScript component allowing integrating an alignment viewer into web pagesAn array of JavaScript objectsFree, GPL 2YesBrowserOfficial website
MaestroYesClustalXYesMapping from sequence to 3D structure, structure-sequence editing-modelingClustal, FASTAPDBProprietary, freeware for academic use??Official website
MEGANoNative ClustalWUPGMA, NJ, ME, MP, with bootstrap and confidence testExtended support to phylogenetics analysisFASTA, Clustal, Nexus, MEGA, etc.Proprietary, freeware, must register??Official website
Molecular Operating Environment (MOE)YesYesYesPart 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_seqProprietary??Official website
MSAReveal.orgNoNoNoOptional 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.FASTAFree, Creative Commons Attribution NonCommercial Share-alike??Official website
Multiseq (VMD plugin)No, but can display and align 3D structuresClustalW, MAFFT, Stamp (Structural)Percent identity, Clustal, MAFFT, StructuralScripting via Tcl, mapping from sequence to 3D structureFASTA, PDB, ALN, PHYLIP, NEXUSProprietary, freeware, but VMD is free for noncommercial use only??Official website
MViewNoNoNoStacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patternsBLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSFFree, GPLNoCross-platform - Mac OS, Linux, WindowsOfficial website
PFAATNo, but can display 3D structuresClustalWNJManual annotation, conservation scoresNexus, MSF, Clustal, FASTA, PFAATProprietary, freeware??Official website
Ralee (emacs plugin for RNA al. editing)?RNA structure??StockholmFree, GPL??Official website
S2S RNA editor2D structureRnalignNoBase-base interactions, 2D-3D viewerFASTA, RnaMLProprietary, freeware??Official website
SeaviewNolocal MUSCLE-ClustalWParsimony, distance methods, PhyMLDot-plot, vim-like editing keysNexus, MSF, Clustal, FASTA, PHYLIP, MASEProprietary, freeware??Official website
SeqotronNoMUSCLE, MAFFTUPGMA, NJ, ML (Physher)Manual alignment, tree visualisationNexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flatFree, GPL?Mac OS XOfficial websitepublication
SequilabYesYesNoLink alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbarsAccession number, GI number, PDB ID, FASTA, drag-drop from external URL from within the user interfaceProprietary, freeware??Official website
SeqPupNo????Proprietary, freeware??Official website
SequlatorNoPairwise alignmentNoeasy alignment editingMSFProprietary, freeware??Official website
SnipVizNoNoNo (but can display them)Pure Javascript and HTML; suitable to integrate in websitesFASTA, newickFree, Apache 2.0YesBrowsersOfficial website, publication
StrapJnet, NNPREDICT, Coiled coil, 16 different TM-helix15 different methodsNJDot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, BioJava-interfaceMSF, Stockholm, ClustalW, Nexus, FASTA, PDB, Embl, GenBank, hssp, PfamFree, GPL??Official website
TabletNoNoNoHigh-performance graphical viewer for viewing next generation sequence assemblies and alignments.ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3Free, BSD 2-clause??Official website
UGENEYesMUSCLE, Kalign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith–Waterman algorithmYesManyFASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFFFree, GPL??Official website
VISSA sequence-structure viewerDSSP secondary structureClustalXNoMapping from sequence to 3D structureClustal, FASTAProprietary, freeware??Official website
DNApyNoMUSCLENoEditing of GenBank files, plasmid drawing, ABI chromatograms,FASTA, FASTQ, GenBankFree, GPL 3??Official website
Alignment AnnotatorYesBy sequence or mixed sequence and structureIncludes ArchaeopteryxDAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview.ManyFree, GPLYesiOS, Android, MS-Mobile,


Official website

See also[edit]

Multiple Sequence Alignment Embl

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