Name | Structure prediction tools integrated | Can align sequences | Can calculate phylogenetic trees | Other features | Format support | License | Can run on Browser | Operating Platforms | Link |
---|---|---|---|---|---|---|---|---|---|
Alan | No | No | No | Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding | FASTA, Clustal | Free, GPL 3 | No | Linux Terminal | Official website |
Ale (emacs plugin) | No | Yes | No | No | GenBank, EMBL, FASTA, PHYLIP | Free, GPL | No | GNU Emacs | Official website |
AliView 2019 | No | MUSCLE integrated; other programs such as MAFFT can be defined | External programs such as FastTree can be called from within | Fast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design. | FASTA, FASTQ, PHYLIP, Nexus, MSF, Clustal | Free, GPL 3 | ? | Cross-platform -Mac OS, Linux, Windows | Official website |
alv | No | No | No | Console-based (no GUI), yet with colors. Coding DNA is coloured by codon. | FASTA, PHYLIP, Nexus, Clustal, Stockholm | Free, GPL 3 | No | Cross-platform | Official website, see also alv on GitHub |
arb | structure editable, show bond in helix sequence regions, 2D molecule viewer | MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference) | 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 visualizes probes. | FASTA, GenBank, EMBL, Newick | Proprietary, freeware, arb license, open modifiable source | No | Linux, Mac OS (homebrew) | Official website |
Base-By-Base | No | MUSCLE | UPGMA, NJ, complete and single linkages, WPMGA | Visual summary, percent identity tables, some integrated advanced analysis tools | Genbank, FASTA, EMBEL, Clustal, base-by-base files | Proprietary, freeware, must register | ? | ? | Official website |
BioEdit | No | ClustalW | Rudimentary, can read PHYLIP | Plasmid drawing, ABI chromatograms, | Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR | Proprietary, freeware | No | Windows (95/98/NT/2000/XP) | Official website |
BioNumerics | No | Yes | Yes | ? | Genbank, FASTA | Proprietary, commercial | ? | ? | Official website |
bioSyntax | No | No | No | Native syntax highlighting support for Vim, less, gedit and Sublime | FASTA, FASTQ, Clustal, SAM, VCF and more | Free, GPL 3 | No | Vim, Less, GEdit, & Sublime | Official website |
BoxShade | No | No | No | Specifically for multiple alignments | MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalW | Free, public domain | No | MSDOS, VMS | Official website |
CINEMA | No, but can read-show 2D structure annotations | ClustalW | No | Dotplot, 6 frame translation, Blast | Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS | Proprietary, freeware | No | Cross-platform -Mac OS, Linux, Windows | Official website |
CLC viewer (free version) | Commercial version only | Clustal, MUSCLE, T-Coffee, MAFFT, Kalign, various | UPGMA, NJ | Workflows, blast-genbank search | many | Proprietary, freeware. More options available in commercial versions. | No | ? | Official website |
ClustalX viewer | No | ClustalW | NJ | Alignment quality analysis | Nexus, MSF, Clustal, FASTA, PHYLIP | Proprietary, freeware for academic use | No | Command line | Official website |
Cylindrical Alignment App | No | No | No | 3D, animation, drilldown, legend selection | BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT | Free, CDDL 1. Available for dual licensing. | ? | Cross-platform -Mac OS, Linux, Windows | Official website |
Cylindrical BLAST Viewer | No | No | No | 3D, animation, drilldown, legend selection | BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT | Free, GPL | ? | ? | Official website |
DECIPHER | Yes | Yes | UPGMA, NJ, ML | Primer-Probe design, Chimera finding | FASTA, FASTQ, GenBank | Free, GPL | No | Mac OS, Windows | Official website |
Discovery Studio | Yes | Align123, ClustalW, S-ALIGN | UPGMA, NJ, with bootstrap and best tree | Visualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, more | BSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT, ... | Proprietary, commercial, Viewer is Freeware | ? | Linux, Windows | Official website |
DnaSP | ? | ? | ? | Can compute several population genetics statistics, reconstruct haplotypes with PHASE | FASTA, Nexus, MEGA, PHYLIP | Proprietary, commercial, freeware for noncomercial use | ? | Cross-platform -Mac OS, Linux, Windows | Official website |
DNASTAR Lasergene Molecular Biology Suite | Yes | Yes | Yes | Align 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, translation | ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred | Proprietary, commercial, academic licenses available | ? | Mac OS, Windows | Official website |
emacs - biomode | ? | ? | ? | ? | ? | Free, GPL | ? | ? | Official website |
FLAK | No | Can perform fuzzy whole genome alignment | No | Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options | FASTA | Proprietary, commercial, freeware for noncommercial use | ? | ? | Official website |
Genedoc | No, but can read-show annotations | Pairwise | No, but can read-show annotations | gel simulation, stats, multiple views, simple | many | Proprietary, freeware | ? | ? | Official websitetable of features |
Geneious | Yes - powered by EMBOSS tools | Clustal, MUSCLE, MAUVE, profile, translation | UPGMA, NJ, PhyML, MrBayes plugin, PAUP* plugin | Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more | >40 file formats imported and exported | Proprietary, commercial; personal, floating | ? | Cross-platform - Mac, Windows, Linux | Official website |
Integrated Genome Browser (IGB) | No | No | No | Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers | BAM, FASTA, PSL | Free, CPL | ? | Cross-platform - Mac, Windows, Linux | Official website |
interactive Tree Of Life (iTOL) | No | No | ? | Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments. | FASTA | Proprietary, free use | Yes | Browser | Official website |
IVisTMSA | No | Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment | Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx | Software 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 calculator | ClustalW, MSF, PHYLIP, PIR, GDE, Nexus | Proprietary, freeware | ? | ? | www.ivistmsa.com |
Jalview | Secondary structure prediction via JNET | Clustal, MUSCLE, MAFFT, Probcons, TCoffee via web services | UPGMA, NJ | Sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL, Uniprot Accession retrieval. | FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm | Free, GPL | Applet | Cross-platform -Mac OS, Linux, Windows | Official website |
Jevtrace | Integrated with structure viewer WebMol | No | No | A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis. | FASTA, MSF, Clustal, PHYLIP, Newick, PDB | Proprietary, commercial, freeware for academic use | ? | Cross-platform -Mac OS, Linux, Windows | Official websitemanual |
JSAV | No | No | No | A JavaScript component allowing integrating an alignment viewer into web pages | An array of JavaScript objects | Free, GPL 2 | Yes | Browser | Official website |
Maestro | Yes | ClustalX | Yes | Mapping from sequence to 3D structure, structure-sequence editing-modeling | Clustal, FASTAPDB | Proprietary, freeware for academic use | ? | ? | Official website |
MEGA | No | Native ClustalW | UPGMA, NJ, ME, MP, with bootstrap and confidence test | Extended support to phylogenetics analysis | FASTA, Clustal, Nexus, MEGA, etc. | Proprietary, freeware, must register | ? | ? | Official website |
Molecular Operating Environment (MOE) | Yes | Yes | Yes | Part 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_seq | Proprietary | ? | ? | Official website |
MSAReveal.org | No | No | No | Optional 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. | FASTA | Free, Creative Commons Attribution NonCommercial Share-alike | ? | ? | Official website |
Multiseq (VMD plugin) | No, but can display and align 3D structures | ClustalW, MAFFT, Stamp (Structural) | Percent identity, Clustal, MAFFT, Structural | Scripting via Tcl, mapping from sequence to 3D structure | FASTA, PDB, ALN, PHYLIP, NEXUS | Proprietary, freeware, but VMD is free for noncommercial use only | ? | ? | Official website |
MView | No | No | No | Stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns | BLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSF | Free, GPL | No | Cross-platform - Mac OS, Linux, Windows | Official website |
PFAAT | No, but can display 3D structures | ClustalW | NJ | Manual annotation, conservation scores | Nexus, MSF, Clustal, FASTA, PFAAT | Proprietary, freeware | ? | ? | Official website |
Ralee (emacs plugin for RNA al. editing) | ? | RNA structure | ? | ? | Stockholm | Free, GPL | ? | ? | Official website |
S2S RNA editor | 2D structure | Rnalign | No | Base-base interactions, 2D-3D viewer | FASTA, RnaML | Proprietary, freeware | ? | ? | Official website |
Seaview | No | local MUSCLE-ClustalW | Parsimony, distance methods, PhyML | Dot-plot, vim-like editing keys | Nexus, MSF, Clustal, FASTA, PHYLIP, MASE | Proprietary, freeware | ? | ? | Official website |
Seqotron | No | MUSCLE, MAFFT | UPGMA, NJ, ML (Physher) | Manual alignment, tree visualisation | Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat | Free, GPL | ? | Mac OS X | Official websitepublication |
Sequilab | Yes | Yes | No | Link alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbars | Accession number, GI number, PDB ID, FASTA, drag-drop from external URL from within the user interface | Proprietary, freeware | ? | ? | Official website |
SeqPup | No | ? | ? | ? | ? | Proprietary, freeware | ? | ? | Official website |
Sequlator | No | Pairwise alignment | No | easy alignment editing | MSF | Proprietary, freeware | ? | ? | Official website |
SnipViz | No | No | No (but can display them) | Pure Javascript and HTML; suitable to integrate in websites | FASTA, newick | Free, Apache 2.0 | Yes | Browsers | Official website, publication |
Strap | Jnet, NNPREDICT, Coiled coil, 16 different TM-helix | 15 different methods | NJ | Dot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, BioJava-interface | MSF, Stockholm, ClustalW, Nexus, FASTA, PDB, Embl, GenBank, hssp, Pfam | Free, GPL | ? | ? | Official website |
Tablet | No | No | No | High-performance graphical viewer for viewing next generation sequence assemblies and alignments. | ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3 | Free, BSD 2-clause | ? | ? | Official website |
UGENE | Yes | MUSCLE, Kalign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith–Waterman algorithm | Yes | Many | FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFF | Free, GPL | ? | ? | Official website |
VISSA sequence-structure viewer | DSSP secondary structure | ClustalX | No | Mapping from sequence to 3D structure | Clustal, FASTA | Proprietary, freeware | ? | ? | Official website |
DNApy | No | MUSCLE | No | Editing of GenBank files, plasmid drawing, ABI chromatograms, | FASTA, FASTQ, GenBank | Free, GPL 3 | ? | ? | Official website |
Alignment Annotator | Yes | By sequence or mixed sequence and structure | Includes Archaeopteryx | DAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview. | Many | Free, GPL | Yes | iOS, Android, MS-Mobile, Browsers | Official website |