Text alignment is a paragraph formatting attribute that determines the appearance of the text in a whole paragraph. For example, in a paragraph that is left-aligned (the most common alignment), text is aligned with the left margin. In a paragraph that is justified, text is aligned with both margins. Align text left. Center text Align text right. Then you add to current alignment, otherwise open new. Find degenerate primers in selected blocks. Configure external programs. Add and configure other alignment programs to use e.g. Install instructions and Downloads: Version history here (versionhistory.txt) Some demo datasets can be found here. Mac OS X (all versions) download here. Org-brain-visualize alignment issue on Mac OS. Ask Question Asked 2 years ago. Active 2 years ago. Viewed 107 times 0.
Available Categories
Select a category to browse .
Administrative
Connection Type
Content type
Operating System
Platform
Products
ID
Title
Views
Posted
Error Displayed on the LCD - TS3520
List of Support Codes for Errors - G620
Support Code 5200 Appears - G620
Support Code 5100 Appears - G620
Support Code 3252 Appears - G620
Support Code 3442 / 3445 Appears - G620
Support Code 3443 / 3444 Appears - G620
Support Code 3440 / 3441 Appears - G620
Support Code 2500 Appears - G620
Support Code 1892 Appears - G620
Support Code 1890 Appears - G620
Support Code 1727 Appears - G620
Support Code 1726 Appears - G620
Support Code 1725 Appears - G620
Support Code 1724 Appears - G620
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, editors[edit]
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 2021
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
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.
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.
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
