Software

From Bioinformatics.Org Wiki

(Difference between revisions)
Jump to: navigation, search
m (S-U)
(External links)
(38 intermediate revisions not shown)
Line 1: Line 1:
-
==0-9==
+
== Popular software for bioinformatics ==
-
* [[3D structure visualization]]
+
Everyday bioinformatics is done with sequence search programs like [[BLAST]], sequence analysis programs, like the [[EMBOSS]] and [[Staden Package|Staden]] packages, structure prediction programs like [[THREADER]] or [[PHD]] or molecular imaging/modelling programs like [[RasMol]] and [[WHAT IF]].
-
==A-C==
+
More:
 +
* [[NetSurfP]] - Protein Surface Accessibility and Secondary Structure Predictions
 +
* [[NetTurnP]] - Prediction of Beta-turn regions in protein sequences
 +
* [[MODELLER]] - Used for homology or comparative modeling of protein three-dimensional structures
 +
* [http://autodock.scripps.edu/ AutoDock] - Suite of Automated Docking Tools
 +
* [http://www.gromacs.org/ Gromacs] - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
-
* [[Applied Biosystems (ABI)]]
+
==  Popular Linux OS distributions for bioinformatics ==
-
* [[Affine gap]]
+
* [http://www.gentoo.org/ Gentoo Linux] ([http://packages.gentoo.org/category/sci-biology?full_cat List of bioinformatics packages])
 +
* [http://bioknoppix.hpcf.upr.edu/ Bioknoppix]
 +
* [http://biopuppy.org BioPuppy] - A Minimal Linux OS for Bioinformatics
 +
* [http://nebc.nox.ac.uk/tools/bio-linux/bio-linux-5.0 BioLinux]
 +
* [http://opendiscovery.org.in Open Discovery] - An integrative bioinformatics linux distro with high performance computing capability
 +
* [http://www.bioslax.com/ Bioslax]
-
* [[Alignment]]
+
Generic yet popular distributions:
 +
* [http://www.ubuntu.com/ Ubuntu]
 +
* [http://fedoraproject.org/ Fedora]
-
* [[Amplification]]
+
==See also==
-
* [[Analytical ultracentrifugation]]
+
* [[:Category:Software]]
 +
* [[Research and development topics]] (including links to software)
 +
* [[Bioinformatics FAQ]]
-
* [[Aneda]]
+
For a list of software (derived from [[SEQwiki]]), click here [[Software/list]].
-
* [[Assembly]]
+
==External links==
-
* [[Base calling]]
+
* [http://www.bioinformatics.org/software/mol_linux.php3 Molecular Linux (original listing)]
-
 
+
* [http://www.facebook.com/pages/SeqChallange/217316754955635 SeqChallenge]
-
* [[Bayesian methods]]
+
* [http://in-silico.net In-Silico Online] Online bioinformatic tools
-
 
+
-
* [[BioCoRE]]
+
-
 
+
-
* [[BLAST]]
+
-
 
+
-
* [[C. elegans]]
+
-
 
+
-
* [[CASP]]
+
-
 
+
-
* [[Chemical kinetics]]
+
-
 
+
-
* [[Chemical structures]]
+
-
 
+
-
* [[Chromatogram]]
+
-
 
+
-
* [[Code generators]]
+
-
 
+
-
* [[Comparative analysis]]
+
-
 
+
-
* [[Comparative genetics]]
+
-
 
+
-
* [[Composition]]
+
-
 
+
-
* [[Correlation]]
+
-
 
+
-
* [[Crystallography]]
+
-
 
+
-
==D-F==
+
-
 
+
-
* [[Data analysis]]
+
-
 
+
-
* [[Data flow]]
+
-
 
+
-
* [[Data mining]]
+
-
 
+
-
* [[Databases]]
+
-
 
+
-
* [[Database interface]]
+
-
 
+
-
* [[Database searching]]
+
-
 
+
-
* [[Database segmentation]]
+
-
 
+
-
* [[Denaturation]]
+
-
 
+
-
* [[Dictionaries]]
+
-
 
+
-
* [[Distance correlations]]
+
-
 
+
-
* [[DNA sequence viewer]]
+
-
 
+
-
* [[DNA sequencing]]
+
-
 
+
-
* [[DNA structure]]
+
-
 
+
-
* [[Drawing]]
+
-
 
+
-
* [[Duplications]]
+
-
 
+
-
* [[Electron density maps]]
+
-
 
+
-
* [[EMBL]]
+
-
 
+
-
* [[EMBOSS]]
+
-
 
+
-
* [[EST]]
+
-
 
+
-
* [[EST clustering similarity alignment]]
+
-
 
+
-
* [[EVA]]
+
-
 
+
-
* [[Evolution]]
+
-
 
+
-
* [[Exons]]
+
-
 
+
-
* [[Extensions]]
+
-
 
+
-
* [[File conversion]]
+
-
 
+
-
* [[Finite elements]]
+
-
 
+
-
* [[Fold recognition]]
+
-
 
+
-
* [[Format converters]]
+
-
 
+
-
==G-I==
+
-
 
+
-
* [[GenBank entry visualization]]
+
-
 
+
-
* [[Gene duplications]]
+
-
 
+
-
* [[Gene expression]]
+
-
 
+
-
* [[Gene finding]]
+
-
 
+
-
* [[Gene regulation]]
+
-
 
+
-
* [[Genetic distances]]
+
-
 
+
-
* [[Genome annotation]]
+
-
 
+
-
* [[Genome development libraries]]
+
-
 
+
-
* [[Genome rearrangement]]
+
-
 
+
-
* [[Genome retrieval]]
+
-
 
+
-
* [[Genomic database system]]
+
-
 
+
-
* [[Genomics]]
+
-
 
+
-
* [[GFF]]
+
-
 
+
-
* [[Global fitting]]
+
-
 
+
-
* [[Graph theory]]
+
-
 
+
-
* [[grep]]
+
-
 
+
-
* [[Group-specific primers]]
+
-
 
+
-
* [[Hidden Markov Models]]
+
-
 
+
-
* [[Homologous genes]]
+
-
 
+
-
* [[Inference]]
+
-
 
+
-
==J-L==
+
-
 
+
-
* [[Java]]
+
-
 
+
-
* [[Libraries]]
+
-
 
+
-
==M-O==
+
-
 
+
-
* [[Maximum likelihood]]
+
-
 
+
-
* [[MCMC]]
+
-
 
+
-
* [[Medline]]
+
-
 
+
-
* [[Melting temperature]]
+
-
 
+
-
* [[Microarray analysis]]
+
-
 
+
-
* [[Modeling]]
+
-
 
+
-
* [[Molecular dynamics]]
+
-
 
+
-
* [[Molecular editors]]
+
-
 
+
-
* [[Molecular graphics]]
+
-
 
+
-
* [[Molecular mechanics]]
+
-
 
+
-
* [[Molecular modeling]]
+
-
 
+
-
* [[Molecular simulations]]
+
-
 
+
-
* [[Molecular structure analysis]]
+
-
 
+
-
* [[Molecular visualization]]
+
-
 
+
-
* [[Molecular weight]]
+
-
 
+
-
* [[Monte Carlo]]
+
-
 
+
-
* [[Motifs]]
+
-
 
+
-
* [[MPI]]
+
-
 
+
-
* [[Multiple]]
+
-
 
+
-
* [[Multiple alignment editors]]
+
-
 
+
-
* [[Multiple genome alignment]]
+
-
 
+
-
* [[Multiple protein structure visualization]]
+
-
 
+
-
* [[Multiple sequence alignment]]
+
-
 
+
-
* [[Multiple sequence alignment drawing]]
+
-
 
+
-
* [[MySQL]]
+
-
 
+
-
* [[NAMD]]
+
-
 
+
-
* [[Neural networks]]
+
-
 
+
-
* [[NMR]]
+
-
 
+
-
* [[Nucleic acids]]
+
-
 
+
-
* [[Oligonucleotides]]
+
-
 
+
-
* [[Online searching]]
+
-
 
+
-
* [[Online tools]]
+
-
 
+
-
==P-R==
+
-
 
+
-
* [[Parallel]]
+
-
 
+
-
* [[Patterns]]
+
-
 
+
-
* [[PCR]]
+
-
 
+
-
* [[PDB]]
+
-
 
+
-
* [[Perl]]
+
-
 
+
-
* [[Phase]]
+
-
 
+
-
* [[Phenotype analysis]]
+
-
 
+
-
* [[Phylogenetics]]
+
-
 
+
-
* [[Phylogenetic trees]]
+
-
 
+
-
* [[Phylogenetic tree reconstruction]]
+
-
 
+
-
* [[Phylogenomics]]
+
-
 
+
-
* [[PostScript]]
+
-
 
+
-
* [[POV-Ray]]
+
-
 
+
-
* [[Prediction]]
+
-
 
+
-
* [[Primers]]
+
-
 
+
-
* [[PROSITE]]
+
-
 
+
-
* [[Protein binding sites]]
+
-
 
+
-
* [[Protein docking]]
+
-
 
+
-
* [[Protein domains]]
+
-
 
+
-
* [[Protein families]]
+
-
 
+
-
* [[Protein interaction]]
+
-
 
+
-
* [[Protein modelling]]
+
-
 
+
-
* [[Protein structure]]
+
-
 
+
-
* [[Protein structure prediction]]
+
-
 
+
-
* [[Protein/DNA/RNA family clustering]]
+
-
 
+
-
* [[PubMed]]
+
-
 
+
-
* [[Python]]
+
-
 
+
-
* [[Real-time visualization]]
+
-
 
+
-
* [[Reannotation]]
+
-
 
+
-
* [[Regular expressions]]
+
-
 
+
-
* [[Regulatory sequence analysis]]
+
-
 
+
-
* [[Rendered animations]]
+
-
 
+
-
* [[RNA]]
+
-
 
+
-
* [[RNA folding]]
+
-
 
+
-
* [[RNA gene finder]]
+
-
 
+
-
* [[RNA motif]]
+
-
 
+
-
* [[RNA pseudoknots]]
+
-
 
+
-
* [[RNA secondary structure]]
+
-
 
+
-
==S-U==
+
-
 
+
-
* [[SCF]]
+
-
 
+
-
* [[Secondary structure]]
+
-
 
+
-
* [[Sequences]]
+
-
 
+
-
* [[Sequence alignment]]
+
-
 
+
-
* [[Sequence analysis]]
+
-
 
+
-
* [[Sequence comparisons]]
+
-
 
+
-
* [[Sequence conversion]]
+
-
 
+
-
* [[Sequence databases]]
+
-
 
+
-
* [[Sequence editor]]
+
-
 
+
-
* [[Sequence finishing]]
+
-
 
+
-
* [[Sequence patterns]]
+
-
 
+
-
* [[Sequence similarity]]
+
-
 
+
-
* [[Sequence utilities]]
+
-
 
+
-
* [[Sequencing]]
+
-
 
+
-
* [[Smith-Waterman]]
+
-
 
+
-
* [[Solid Angle calculation]]
+
-
 
+
-
* [[Statistical mechanics]]
+
-
 
+
-
* [[Steric size calculation]]
+
-
 
+
-
* [[Structural alignments]]
+
-
 
+
-
* [[Structural biology]]
+
-
 
+
-
* [[Structure]]
+
-
 
+
-
* [[Structure analysis]]
+
-
 
+
-
* [[Structure prediction]]
+
-
 
+
-
* [[Substitution]]
+
-
 
+
-
* [[Substitution rates]]
+
-
 
+
-
* [[SwissProt]]
+
-
 
+
-
* [[Tcl/Tk]]
+
-
 
+
-
* [[Thermodynamics]]
+
-
 
+
-
* [[Threading]]
+
-
 
+
-
* [[Trace]]
+
-
 
+
-
* [[Trace chromatogram]]
+
-
 
+
-
* [[Trace files]]
+
-
 
+
-
* [[Trajectory analysis]]
+
-
 
+
-
* [[Transcription factors]]
+
-
 
+
-
* [[Trees]]
+
-
 
+
-
* [[Tree of life]]
+
-
 
+
-
* [[Tree viewers]]
+
-
 
+
-
* [[tRNA searching]]
+
-
 
+
-
==V-Z==
+
-
 
+
-
* [[Visualization]]
+
-
 
+
-
* [[VMD]]
+
-
 
+
-
* [[Web robots]]
+
-
 
+
-
* [[Workflow]]
+

Revision as of 11:55, 28 July 2011

Contents

Popular software for bioinformatics

Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHAT IF.

More:

Popular Linux OS distributions for bioinformatics

Generic yet popular distributions:

See also

For a list of software (derived from SEQwiki), click here Software/list.

External links

Personal tools
Namespaces
Variants
Actions
wiki navigation
Toolbox