List of alignment visualization software

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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.

Alignment viewers, editorsEdit

Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Allows
sequence
alignments to
be viewed
FASTA,
Alan No No No quickly and Free, GPL 3 No
Clustal
directly in a
linux terminal
without X-
forwarding

GenBank,
Ale (emacs EMBL,
No Yes No No Free, GPL No
plugin) FASTA,
PHYLIP

Fast, easy
navigation
through
unlimited FASTA,
MUSCLE External
mouse wheel FASTQ,
integrated; other programs such
zoom in-out PHYLIP,
AliView 2021 No programs such as as FastTree Free, GPL 3 ?
feature. Nexus,
MAFFT can be can be called
Handles MSF,
defined from within
unlimited file Clustal
size alignments.
Degenerate
primer design.

Console-based
FASTA,
(no GUI), yet
PHYLIP,
with colors.
alv No No No Nexus, Free, GPL 3 No
Coding DNA is
Clustal,
coloured by
Stockholm
codon.
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Edits huge
alignments and
trees. Supports
NUCs + AA.
structure
MUSCLE, MAFFT, Displays codons
editable, arb-parsimony
ClustalW, below DNA. Proprietary,
show bond & -NJ, RAxML, FASTA,
ProbCons, Custom column freeware, arb
in helix PHYML, GenBank,
arb FastAligner highlighting license, open No
sequence Phylip, EMBL,
(region- (e.g. by modifiable
regions, 2D FastTree2, Newick
align+auto- conservation source
molecule MrBayes
reference) profiles).
viewer
Designs,
matches and
visualizes
probes.

Visual
Genbank,
UPGMA, NJ, summary,
FASTA,
complete and percent identity Proprietary,
EMBEL,
Base-By-Base No MUSCLE single tables, some freeware, must ?
Clustal,
linkages, integrated register
base-by-
WPMGA advanced
base files
analysis tools

Genbank,
Rudimentary, Plasmid FASTA,
Proprietary,
BioEdit No ClustalW can read drawing, ABI PHYLIP 3.2 No
freeware
PHYLIP chromatograms, and 4,
NBRF-PIR

Genbank, Proprietary,
BioNumerics No Yes Yes ? ?
FASTA commercial

Native syntax FASTA,

highlighting FASTQ,
bioSyntax No No No support for Clustal, Free, GPL 3 No
Vim, less, gedit SAM, VCF
and Sublime and more

MSF format
as written
by PILEUP,
READSEQ,
Specifically for
or SEQIO Free, public
BoxShade No No No multiple No
(fmtseq); domain
alignments
ALN
format as
written by
ClustalW

Nexus,
No, but can MSF,
read-show Dotplot, 6 frame Clustal,
Proprietary,
CINEMA 2D ClustalW No translation, FASTA, No
freeware
structure Blast PHYLIP,
annotations PIR,
PRINTS

Proprietary,
freeware. More
Clustal, MUSCLE, Workflows,
CLC viewer Commercial options
T-Coffee, MAFFT, UPGMA, NJ blast-genbank many No
(free version) version only available in
Kalign, various search
commercial
versions.

Alignment
visualisation as
publication-
CIAlign No No No FASTA Free, MIT No
ready images,
alignment
cleaning.
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Nexus,
MSF, Proprietary,
ClustalX Alignment
No ClustalW NJ Clustal, freeware for No
viewer quality analysis
FASTA, academic use
PHYLIP

BLAST
XML,
proprietary
3D, animation, XML, GFF3, Free, CDDL 1.
Cylindrical
No No No drilldown, ClustalW, Available for ?
Alignment App
legend selection INSDSet, dual licensing.
user
expandable
with XSLT

BLAST
XML,
proprietary
3D, animation, XML, GFF3,
Cylindrical
No No No drilldown, ClustalW, Free, GPL ?
BLAST Viewer
legend selection INSDSet,
user
expandable
with XSLT

Primer-Probe FASTA,
UPGMA, NJ,
DECIPHER Yes Yes design, Chimera FASTQ, Free, GPL No
ML
finding GenBank

Visualizer
supports 2D and
BSML,
3D structure
EMBL, GB,
and sequence; Proprietary,
Align123, UPGMA, NJ, HELM,
Discovery full version has commercial,
Yes ClustalW, S- with bootstrap Clustal, ?
Studio comprehensive Viewer is
ALIGN and best tree FASTA,
functionality Freeware
GDE, PDB,
for protein,
SEQ, SPT, ...
nucleotides,
more

Can compute
several
Proprietary,
population FASTA,
commercial,
genetics Nexus,
DnaSP ? ? ? freeware for ?
statistics, MEGA,
noncomercial
reconstruct PHYLIP
use
haplotypes with
PHASE

Align DNA,
RNA, protein, or
DNA + protein
sequences via a
variety of
pairwise and
multiple
sequence
alignment ABI, DNA
Proprietary,
DNASTAR algorithms, Multi-Seq,
commercial,
Lasergene generate FASTA, GCG
Yes Yes Yes academic ?
Molecular phylogenetic Pileup,
licenses
Biology Suite trees to predict GenBank,
available
evolutionary Phred
relationships,
explore
sequence tracks
to view GC
content, gap
fraction,
sequence logos,
translation

emacs -
? ? ? ? ? Free, GPL ?
biomode
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Very fast, highly

Proprietary,
Can perform customisable,
commercial,
fuzzy whole visualisation is
FLAK No No FASTA freeware for ?
genome WYSIWYG with
noncommercial
alignment filtering and
use
fuzzy options

No, but can No, but can gel simulation,

Proprietary,
Genedoc read-show Pairwise read-show stats, multiple many ?
freeware
annotations annotations views, simple

Whole genome
UPGMA, NJ, assembly, >40 file
Yes - Proprietary,
Clustal, MUSCLE, PhyML, restriction formats
powered by commercial;
Geneious MAUVE, profile, MrBayes analysis, imported ?
EMBOSS personal,
translation plugin, PAUP* cloning, primer and
tools floating
plugin design, dotplot, exported
much more

Sequences and
features from
Integrated
files, URLs, and BAM,
Genome No No No Free, CPL ?
arbitrary DAS FASTA, PSL
Browser (IGB)
and QuickLoad
servers

Phylogenetic
tree viewer-
annotation tool
which can
visualise
interactive alignments
Proprietary,
Tree Of Life No No ? directly on the FASTA Yes
free use
(iTOL) tree. Various
other dataset
types can be
displayed in
addition to
alignments.

Software is
package of 7
interactive
visual tools for
multiple
Tree sequence
calculation alignments.
Clustal Omega,
tool calculates Major focus is
ClustalW2, ClustalW,
phylogenetic manipulating
MAFFT, MUSCLE, MSF,
tree using large Proprietary,
IVisTMSA No BioJava are PHYLIP, ?
BioJava API alignments. freeware
integrated to PIR, GDE,
and lets user Includes
construct Nexus
draw trees MSApad, MSA
alignment
using comparator,
Archaeopteryx MSA
reconstruction
tool, FASTA
generator and
MSA ID matrix
calculator
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Sequences and
FASTA,
features
Pfam, MSF,
retrieved from
Clustal,
user-
BLC, PIR,
configurable
Stockholm,
and publicly
VCF, AMSA,
registered
Clustal O, Clustal, BioJSON,
servers, e.g.
GLprobs, Clustal,
Secondary EMBL, EBI, PDB,
MSAprobs, ENA,
structure Pfam, Rfam, JalviewJS
Jalview MUSCLE, MAFFT, UPGMA, NJ GenBank, Free, GPL
prediction UniProt (Javascript)
Probcons, GFF2,
via JPred 4 Accession
TCoffee, via web GFF3,
retrieval.
services JnetFile,
Structure/model
PHYLIP,
data retrieval
PileUp,
from PDB and
RNAML,
3D-Beacons
CIF,
including PDBe,
mmCIF,
AlphaFold DB,
PDB.
SWISS-MODEL.

A multivalent
browser for
sequence
alignment,
FASTA,
Integrated phylogeny, and
MSF, Proprietary,
with structure.
Clustal, commercial,
Jevtrace structure No No Performs an ?
PHYLIP, freeware for
viewer interactive
Newick, academic use
WebMol Evolutionary
PDB
Trace and other
phylogeny
inspired
analysis.

A JavaScript
component
allowing An array of
JSAV No No No integrating an JavaScript Free, GPL 2 Yes
alignment objects
viewer into web
pages

Native desktop
alignment
Proprietary,
viewer, uses BAM,
commercial,
Lucid Align No No No trackpad/mouse FASTQ, No
freeware for
gestures. Allows FASTA
academic use
streaming
remote data

Mapping from
sequence to 3D
structure, Proprietary,
Clustal,
Maestro Yes ClustalX Yes structure- freeware for ?
FASTA PDB
sequence academic use
editing-
modeling

UPGMA, NJ,
Extended FASTA,
ME, MP, with Proprietary,
support to Clustal,
MEGA No Native ClustalW bootstrap and freeware, must ?
phylogenetics Nexus,
confidence register
analysis MEGA, etc.
test

Part of an
extensive Clustal,
collection of FASTA,
applications for PDB, EMBL,
Molecular
sequence to GCG,
Operating
Yes Yes Yes structure, GCG_MSF, Proprietary ?
Environment
including Genbank,
(MOE)
homology PHYLIP,
modelling; 3D PIR,
visualisation, raw_seq
etc.
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Optional
coloring.
Touching AA
shows 3-letter
code and
sequence
Free, Creative
number.
Commons
Touching
[Link] No No No FASTA Attribution ?
consensus
NonCommercial
shows AA
Share-alike
frequencies in
that column.
Counts and
percentages of
aromatics,
charged, gaps.

Percent Proprietary,
No, but can Scripting via FASTA,
ClustalW, MAFFT, identity, freeware, but
Multiseq (VMD display and Tcl, mapping PDB, ALN,
Stamp Clustal, VMD is free for ?
plugin) align 3D from sequence PHYLIP,
(Structural) MAFFT, noncommercial
structures to 3D structure NEXUS
Structural use only

Stacked
alignments BLAST
from blast and search,
fasta suites, FASTA
various MSA search,
MView No No No Free, GPL No
format Clustal,
conversions, HSSP,
HTML markup, FASTA, PIR,
consensus MSF
patterns

Nexus,
Manual
No, but can MSF,
annotation, Proprietary,
PFAAT display 3D ClustalW NJ Clustal, ?
conservation freeware
structures FASTA,
scores
PFAAT

Ralee (emacs
plugin for RNA ? RNA structure ? ? Stockholm Free, GPL ?
al. editing)

Base-base
2D FASTA, Proprietary,
S2S RNA editor Rnalign No interactions, 2D- ?
structure RnaML freeware
3D viewer

Nexus,
Parsimony, MSF,
local MUSCLE- distance Dot-plot, vim- Clustal, Proprietary,
Seaview No ?
ClustalW methods, like editing keys FASTA, freeware
PhyML PHYLIP,
MASE

Nexus,
Clustal,
FASTA,
Manual
UPGMA, NJ, PHYLIP,
Seqotron No MUSCLE, MAFFT alignment, tree Free, GPL ?
ML (Physher) MEGA,
visualisation
Stockholm,
NBRF/PIR,
GDE flat
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

Link alignment
Accession
results to
number, GI
analysis tools
number,
(Primer design,
PDB ID,
Gel mobility
FASTA,
and Maps,
drag-drop Proprietary,
Sequilab Yes Yes No Plasmapper, ?
from freeware
siRNA design
external
Epitope
URL from
prediction),
within the
Save research
user
logs, Create
interface
custom toolbars

Proprietary,
SeqPup No ? ? ? ? ?
freeware

Pairwise easy alignment Proprietary,

Sequlator No No MSF ?
alignment editing freeware

Pure Javascript
and HTML;
No (but can FASTA,
SnipViz No No suitable to Free, Apache 2.0 Yes
display them) newick
integrate in
websites

Dot-plot,
structure-
MSF,
neighbors, 3D-
Stockholm,
Jnet, superposition,
ClustalW,
NNPREDICT, Blast-search,
15 different Nexus,
Strap Coiled coil, NJ Mutation-SNP Free, GPL ?
methods FASTA,
16 different analysis,
PDB, Embl,
TM-helix Sequence
GenBank,
features,
hssp, Pfam
BioJava-
interface

High-
performance ACE, AFG,
graphical MAQ,
viewer for SOAP2,
Free, BSD 2-
Tablet No No No viewing next SAM, BAM, ?
clause
generation FASTA,
sequence FASTQ,
assemblies and GFF3
alignments.

FASTA,
FASTQ,
MUSCLE, Kalign, GenBank,
ClustalW, EMBL,
ClustalO, ClustalX, ABIF, SCF,
UGENE Yes Yes Many Free, GPL ?
MAFFT, T-Coffee, ClustalW,
Smith–Waterman Stockholm,
algorithm Newick,
PDB, MSF,
GFF

VISSA
DSSP Mapping from
sequence- Clustal, Proprietary,
secondary ClustalX No sequence to 3D ?
structure FASTA freeware
structure structure
viewer

Editing of
GenBank files, FASTA,
DNApy No MUSCLE No plasmid FASTQ, Free, GPL 3 ?
drawing, ABI GenBank
chromatograms,
 Structure
Can calculate
prediction Can align Format Can run on
Name phylogenetic Other features License
tools sequences support Browser
trees
integrated

DAS and user

defined
By sequence or annotations.
Alignment Includes
Yes mixed sequence Scriptable. Many Free, GPL Yes
Annotator Archaeopteryx
and structure Export to
HTML, Word,
Jalview.

See alsoEdit