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Multiple alignment visualization tools typically serve four purposes:
* General comprehension of large-scale DNA or protein alignments
* Visualization of alignments for figures and publication.
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! Other Features
! Formats Supported
! License
! Link
|-
| Ale (emacs plugin)
| No
| Yes
| No
| No
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| Muscle
| UPGMA, NJ, Complete Linkage, Single Linkage, WPMGA
| Visual summary, percent identity tables, some integrated advanced analysis tools
| Genbank, Fasta, EMBEL, Clustal, Base-by-base files
| Free, registration required
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| ClustalW
| rudimentary, can read phylip
| plasmid drawing, ABI chromatograms,
| Genbank, Fasta, Phylip 3.2, Phylip 4, NBRF/PIR
| Free
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| Yes
| Yes
|
| Genbank, Fasta
| Commercial
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| No
| Specifically for multiple alignments
| MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq).
| Public ___domain
| [http://ch.embnet.org/software/BOX_form.html link]
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|-
| DnaSP
|
|
|
| can compute several population genetics statistics, reconstruct haplotypes with PHASE
| [[FASTA]], [[Nexus file|Nexus]], Mega, [[PHYLIP]]
| [[Freeware]]
|
|-
| emacs - biomode
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|-
| PFAAT
| NO, but can display 3D structures
| ClustalW
| [[Neighbor-joining]]
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|-
| Ralee (emacs plugin for RNA al. editing)
|
| RNA structure
|
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|-
| S2S RNA editor
| 2D structure
| Rnalign
| No
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|
| [http://pbil.univ-lyon1.fr/software/seaview.html link]
|-
| 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
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| SeqPop
| No
|
|
|
|
| Free
| [http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/ link]
|-
| Strap
| Jnet, NNPREDICT, Coiled coil,
| Fifteen different Methods
| [[Neighbor-joining]]
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| [[MSF format|MSF]], [[Stockholm format|Stockholm]], [[Clustal]]w, [[Nexus file|Nexus]], [[FASTA]], [[Protein Data Bank (file format)|PDB]], Embl, [[GenBank]], [[hssp]], [[Pfam]]
| [[GPL]]
|
|-
| [[UGENE]]
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| Yes
| Mapping from sequence to 3D structure, structure/sequence editing/modeling
| [[Clustal]], [[FASTA format|FASTA]] [[Protein Data Bank|
| Free for Academics
| [http://www.schrodinger.com/products/14/12/ link]
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==See also==
* [[Sequence alignment software]]
* [[Biological data visualization]]
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