CLC Sequence Viewer is Bioinformatics analysis and data management for OS X 10.4 or Later.
A Sequence Viewer for basic bioinformatics
CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.
The software package is a community edition, available for Windows, Mac OS X, and Linux. Download is free of charge.
These are the top five reasons to try CLC Sequence Viewer
1. You will have easy access to a large number of integrated research tools:
* Creating and editing alignments
* Interactive restriction site analysis
* Phylogenetics
* Integrated GenBank searches
* Advanced DNA to Protein translation
* And many more
2. You can get easy access to hardware accelerated database searches
* Plug in the Bioinformatics Cube and increase your search speed up to 200 times
3. Your research work will be easy to carry out
* The program is graphically based, intuitive, and user-friendly
4. You will have a bioinformatics solution that continuously evolves
* The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
5. You will get superior customer service
* We offer free support to all users - also users of our free demo version
Product features:
Bioinformatics features in CLC Sequence Viewer
* Multiple alignment of DNA, RNA, and proteins
o Two proprietary algorithms
o ClustalW
o Muscle
o T-Coffee
o MAFFT
o Kalign
* Consensus sequence determination and management
* Conservation score along alignments
* Open reading frame determination
* Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
* Translation from DNA to proteins (all genetic translation tables)
* Reports with residue composition, molecular weight and iso electric point (for proteins)
* Neighbor-joining and UPGMA phylogenies
* Restriction site analysis and viewing
* Create reverse complement
* Shuffle sequence
* Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio
Other features in CLC Sequence Viewer
* Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
* All types of files can be saved in local projects and launched from the program
* Detailed history log
* User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
* Text-based sequence view
* Easy printing of reports and graphics
* Export of user-defined figures to various graphics file formats
* Import and export of data in a large number of file formats
* Option of working with different files and in different file projects at the same time
* Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
Handling of different file formats
CLC Sequence Viewer is very versatile when it comes to importing and exporting both data and graphics files. To name a few, you can export graphics as PNG, PDF, or EPS. Import data from Vector NTI, CLUSTAL W, or DNA Strider. And among others GenBank, Fasta, Swiss-Prot, UniProt and EMBL formats are supported for both im- and export.
File formats:
File type Suffix File format used for
ACE files .ace contigs (only import)
Phylip Alignment .phy alignments
GCG Alignment .msf alignments
Clustal Alignment .aln alignments
Newick .nwk trees
FASTA .fsa/.fasta sequences
GenBank .gbk/.gb/.gp sequences
GCG sequence .gcg sequences (only import)
PIR (NBRF) .pir sequences (only import)
Staden .sdn sequences (only import)
DNAstrider .str/.strider sequences
Swiss-Prot .swp protein sequences
Lasergene sequence .pro protein sequence (only import)
Lasergene sequence .seq nucleotide sequence (only import)
Embl .embl nucleotide sequences
Nexus .nxs/.nexus sequences, trees, alignments, and sequence lists
CLC .clc sequences, trees, alignments, reports, etc.
Text .txt all data in a textual format
CSV .csv tables, each cell separated with semicolons (only export)
ABI .abi trace files (only import)
AB1 .ab1 trace files (only import)
SCF2 .scf trace files (only import)
SCF3 .scf trace files (only import)
Phred .phd trace files (only import)
mmCIF .cif structure (only import)
PDB .pdb structure (only import)
BLAST Database .phr/.nhr BLAST database (import)
Vector NTi Database sequences (import of whole database)
VectorNTI achieves .ma4/.pa4/.oa4 sequences (only import)
Gene Construction Kit .gcc sequences (only import)
RNA Structure .ct/.col/.rnaml/.xml RNA structures
Preferences .cpf CLC preferences
I believe this requires free registration. Santa frowns on programs that require you to do more than download and play but this is the only sequence reader he features. Hey - if you know what this is and you need it I'm sure you won't mind registration.
http://clcbio.com/index.php?id=479