|
|
Software |
Free/ Commercial |
Website |
Functions of the software |
|
Visualization |
|
1. |
Rasmol |
Free |
http://www.bernstein-plus-sons.com/ software/rasmol |
-
Popular and versatile molecular graphics viewing program, excellent for
viewing macromolecular structures
-
Needs
command line scripting
|
|
2. |
Weblab lite |
Free |
http://www.accelrys.com/viewer/t |
-
Molecular Visualization, Analysis and structural information
-
No
command line scripting
|
|
Suite |
|
3. |
Bioedit |
Freeware |
http://www.mbio.ncsu.edu/BioEdit/bioedit.html |
-
Biological sequence alignment editor
-
Automated ClustalW alignment
-
Plasmid drawing and annotation
-
Accessory application configuration
-
Restriction mapping
-
RNA
comparative analysis tools
-
Graphical matrix data viewing tools
-
Shaded
alignment figures
-
Translation-based nucleic acid alignment
-
ABI
trace viewing, editing and printing
-
Web
integration
|
|
4. |
Antherpr
ot |
Freeware |
http://antheprot-pbil.ibep.fr/ie_sommaire.html |
-
Sequence information
-
Sequence edition
-
Dot
matrix plot
-
Fasta/Blast
-
Sites/signatures detection
-
Physico-chemical profiles
-
Secondary structure prediction
-
Helical wheel projections
-
Binary
alignments (dynamic programming NW algorithm)
-
Multiple alignments
-
Prediction of signal peptide and cleavage site
-
3D
display of molecules
-
Amphiphilicity
-
Titration curve
|
|
5. |
DNA tools |
Freeware (but license is
needed) |
http://www.dnatools.dk |
-
Handling and analysis of nucleotide and protein sequences
-
Sequence editing and annotation, restriction mapping, translation, batch
blast search, codon analysis, primer design and ordering handling
-
Analysis of small EST projects and SAGE data
|
|
Miscellaneous |
|
1. |
Winpep |
Freeware |
http://www.ipw.agrl.ethz.ch/~lhennig/winpep.html |
-
Determination of length and amino acid composition
-
Calculation of the molecular weight
-
Estimation of the isoelectric point (IEP)
-
Estimation of molar absorption coefficients
-
Batch
analysis of multiple sequences
-
Simulation of sequences specific cleavage
-
Identification of potential post-translational modifications
-
Searching for sequence motifs
-
Helical wheel display of amino acid sequences
-
Hydropathy plot display of sequences
-
Display of the domain structure of proteins.
|
|
2. |
DNA for windows |
Freeware |
http://website.lineone.net/~molbio |
-
Easy
manipulation of sequences - removal of ‘junk’ text, reverse, complement,
trim, etc.
-
Restriction enzyme analysis - custom groups of enzymes
-
Translation of DNA to protein
-
Calculates mass of selected protein.
-
Easy
multiple sequence alignment
-
Automatic contig assembly-using interface to CAP program
-
Dot-Plot analysis
|
|
3. |
ClustalX |
Freeware |
Http://inn-prot.weizmann.ac.il/ software/ClustalX.html |
-
Multiple sequence alignment program with user friendly interface
|
|
4. |
Cluster |
Freeware, but needs
license |
Http://rana.lbl.gov/EisenSoftware.htm |
-
Cluster analysis and microarray dataset processing–hierarchical
clustering, self-organizing maps (SOMs), k-means clustering, principal
componenet analysis
|
|
5. |
Treeview |
Freeware, but needs
license |
http://rana.lbl.gov/EisenSoftware.htm |
-
Graphically representation of clustering and other analyses from
Cluster.
|
|
6. |
Treeview |
Freeware |
http://taxonomy.zoology.gla.ac.uk /rod/treeview.html |
-
Phylogeny tree drawing software
|
|
7. |
LINDO |
Commercial/demo version |
www.lindo.com |
-
Linear
Programming Package, suitable for optimization
-
Can be
used for flux balance analysis (FBA).
|
