Bioinformatics resource list
From Christoph's Personal Wiki
This article will contain a list of useful resources for bioinformaticians (or computational biologists, or scientists in general). It will list software, libraries, web servers, general data, and any other resource I find useful.
Not all resources listed here are open source. Since I am a firm believer in open source, I will eventually remove those resources listed below that are not open source in favour of those that are. This means they should be at least:
- GPL/LGPL;
- able to download from any machine (i.e. including non-academic);
- able to use for any purpose;
- zero registration required (not even an email address);
- absolutely must work on Linux;
- the source files must be included (i.e. not just the binaries);
- preferably CLI-friendly (i.e. able to run entirely from the command-line); and
- preferably STDIN/STDOUT streams (i.e. input can be a pipe stream; in/out filenames are not arguments)
Contents
- 1 Application/Bioinformatics
- 2 Application/Engingeering
- 3 Applications/Bioinformatics
- 4 Applications/Engineering
- 5 Applications/Graphics
- 6 Applications/Internet
- 7 Applications/Mail
- 8 Applications/Math
- 9 Applications/Multimedia
- 10 Applications/Science
- 11 Applications/System
- 12 Bioinformatics/SequenceAnalysis
- 13 Development/Debuggers
- 14 Development/Languages
- 15 Development/Libraries
- 16 Development/Tools
- 17 Graphics
- 18 Libraries
- 19 Scientific/Cluster
- 20 Scientific/Engineering
- 21 System Environment/Libraries
- 22 Miscellaneous
- 23 Molecular docking resources
- 24 External links
Application/Bioinformatics
- 3ddock
- A suite of automated docking tools. (License: Cancer Research UK)
- CHARMM
- CHARMM - Molecular Dynamics Package. (License: Harvard University)
- amber
- A package of molecular simulation programs. (License: UCSF)
- chimera
- UCSF Chimera - A molecular viewer and analysis program. (License: UCSF)
- dms
- DMS - Molecular Surface Program. (License: UCSF)
- dock
- UCSF DOCK - A molecular docking program. (License: UCSF)
- gold
- Protein-Ligand Docking. (License: CCDC)
- insightII
- Ensemble Molecular Modeling Package. (License: Accelrys)
- libpdb
- The library needed for PDB files read by the dms program. (License: UCSF)
- mfold
- RNA and DNA secondary structure prediction. (License: GPL)
- pdb_h
- The header needed for PDB files read by the dms program. (License: UCSF)
- sybyl
- Ensemble Molecular Modeling Package. (License: Tripos)
Application/Engingeering
- CCP4mg
- The CCP4 Molecular Graphics Program. (License: ccp4.ac.uk)
- ImageJ
- A Java Image Manipulation Tool. (License: GPL)
- alfresco
- Comparative Genome Sequence Analysis Tool. (License: GPL)
- artemis
- DNA sequence viewer and annotation tool. (License: GPL)
- autodock
- A suite of automated docking tools. (License: The Scripps Research Institute)
- cn3d
- Molecular Graphics Visualization Tool. (License: GPL)
- connolly
- Molecular Surface Program. (License: Indiana University)
- delphi
- DelPhi - A Finite Difference Poisson-Boltzman Solver. (License: Columbia University
- dotlet
- A diagonal dot-plot tool. (License: GPL)
- dssp
- Program to standardize secondary structure assignment. (License: GPL)
- genemine
- Look/GeneMine. (License: GPL)
- jackal
- JACKAL: A protein structure modeling package. (License: GPL)
- jalview
- A Java Sequence Alignment Viewer. (License: GPL)
- mage
- Molecular Graphics Visualization Tool. (License: GPL)
- mgltools
- A suite of automated docking tools. (License: Michael Sanner and TSRI)
- moe
- Molecular Operating Environment. (License: Chemical Computing Group)
- molauto
- A program for producing good first-approximation MolScript input files. (License: Avatar Software)
- molscript
- A program for displaying molecular 3D structures. (License: Avatar Software AB)
- msms
- Computes, for a given probe radius, the reduced surface of a set of spheres. (License: GPL)
- namd
- Not Another Molecular Dynamics. (License: Univ of Illinois)
- procheck
- Programs to check the Stereochemical Quality of Protein Structures. (License: EBI)
- rasmol
- Molecular Graphics Visualization Tool. (License: GPL)
- spdbv
- Swiss-Prot DeepView. (License: GPL)
- stc
- Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 catalytic subunit and microcystin-LR docked complexes. (License: GPL)
- vmd
- Visualization and analysis tool of biological systems. (License: Univ of Illinois)
- x3dna
- 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. (License: GPL)
- xpvm
- A GUI interface for PVM, Parallel-Virtual Machine. (License: GPL)
Applications/Bioinformatics
- DOMAINATRIX
- EMBOSS:DOMAINATRIX Applications. (License: GPL)
- DOMALIGN
- EMBOSS:DOMALIGN Applications. (License: GPL)
- DOMSEARCH
- EMBOSS:DOMSEARCH Applications. (License: GPL)
- EMBOSS
- The European Molecular Biology Open Software Suite. (License: GPL/LGPL)
- EMBOSS-Jemboss
- Java based GUI for EMBOSS. (License: GPL/LGPL)
- EMBOSS-data
- Extra data for EMBOSS. (License: GPL/LGPL)
- EMNU
- EMBOSS:EMNU Applications. (License: GPL)
- ESIM4
- EMBOSS:ESIM4 Applications. (License: GPL)
- ESTScan
- Program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. (License: Copyright SIB, LICR and ISREC 1999)
- HMMER
- EMBOSS:HMMER Applications. (License: GPL)
- MEMENEW
- EMBOSS:MEMENEW Applications. (License: GPL)
- MSE
- EMBOSS:MEME Applications. (License: GPL)
- MYEMBOSS
- EMBOSS:MYEMBOSS Applications. (License: GPL)
- PHYLIPNEW
- EMBOSS:PHYLIP Applications. (License: GPL)
- SIGNATURE
- EMBOSS:SIGNATURE Applications. (License: GPL)
- STRUCTURE
- EMBOSS:STRUCTURE Applications. (License: GPL)
- TOPO
- EMBOSS:TOPO Applications. (License: GPL)
- VIENNA
- EMBOSS:VIENNA Applications. (License: GPL)
- blat
- Basic Local Alignment Tool. (License: LGPL)
- gibbs
- Gibbs motif sampler. (License: Public Domain)
- hbplus
- A program for hydrogen bond calculation. (License: biochem.ucl.ac.uk)
- ligplot
- A program for automatically plotting protein-ligand interactions. (License: biochem.ucl.ac.uk)
- paml
- Phylogenetic analyses of DNA or protein sequences using maximum likelihood. (License: free for academic use only)
- phrap
- phragment assembly program. (License: Phil Green)
- primer3
- Primer3 picks primers for PCR reactions. (License: Copyright Whitehead Institute for Biomedical Research)
- repeatmasker
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. (License: GPL)
- seaview
- Graphical multiple alignment editor. (License: Freely available to all end users)
- sim4
- Program to align cDNA and genomic DNA. (License: GPL)
- tree
- Maximum likelihood analysis for nucleotide, amino acid and two-state data. (License: GPL)
Applications/Engineering
- R
- A statistical computation and graphics system. (License: GNU)
- matlab
- Matlab 7, Release 14 Service Pack 2. (License: 2005 Matlab)
- modeller
- Protein structure modeling by satisfaction of spatial restraints. (License: Academic)
- openbabel
- A free, open-source version of the Babel chemistry file translation program. (License: GPL)
Applications/Graphics
- gsview
- PostScript and PDF previewer. (License: Aladdin Free Public License, Ghostgum Software Pty Ltd)
Applications/Internet
- flash-plugin
- Macromedia Flash Plug-In for Mozilla-Firefox. (License: GPL)
- j2re-plugin
- Java 2 Plug-In for Mozilla-Firefox. (License: GPL)
Applications/Mail
- pine
- University of Washington Pine mail user agent. (License: see file CPYRIGHT)
Applications/Math
- grace
- Numerical Data Processing and Visualization Tool (grace). (License: GPL)
Applications/Multimedia
- gd-progs
- Utility programs that use libgd. (License: BSD-style)
Applications/Science
- gromacs
- Molecular dynamics package (non-parallel version). (License: GPL)
- gromacs-devel
- Header files and static libraries for GROMACS. (License: GPL)
Applications/System
- gnupg
- A GNU utility for secure communication and data storage. (License: GPL)
Bioinformatics/SequenceAnalysis
- footprinter
- A program that performs phylogenetic footprinting. (License: 1999-2002 Mathieu Blanchette and Martin Tompa)
Development/Debuggers
- xxgdb
- An X Window System graphical interface for the GNU gdb debugger. (License: MIT)
Development/Languages
- icm-browser
- The ICM (Internal Coordinate Mechanics) software project. (License: Molsoft L.L.C)
- icmbrowser-desktop
- Menu Item for ICM-Browser. (License: Molsoft L.L.C)
- intel-ifort8
- Intel(R) Fortran Compiler for 32-bit applications, Version 8. (License: Intel(R) Copyright 2003)
- molsoft
- ICM-Browser Support. (License: UMDNJ 2004)
Development/Libraries
- EMBOSS-devel
- Header files and static libraries for EMBOSS. (License: GPL/LGPL)
- NCBI-devel
- The development libraries and header files for ncbi. (License: GPL)
- fftw-devel
- headers, libraries, and docs for FFTW fast fourier transform library. (License: GPL)
- fftw3-devel
- Headers, libraries and docs for the FFTW library. (License: GPL)
- gd-devel
- The development libraries and header files for gd. (License: BSD-style)
- perl-RNA
- Vienna RNA package Perl module. (License: Free for non-commercial use)
Development/Tools
- blt
- A Tk toolkit extension. (License: MIT)
- jdk
- Java(TM) 2 Platform Standard Edition Development Kit. (License: Sun Microsystems Binary Code License (BCL))
- jdk-path
- Java 2 SDK Path Modifier. (License: GPL)
Graphics
- Raster3D
- Raster3D photorealistic molecular graphics package. (License: Source freely available, redistribution restricted)
Libraries
- fftw
- fast fourier transform library. (License: GPL)
- netcdf
- Libraries to use the Unidata network Common Data Form (netCDF). (License: distributable)
- pdflib
- Portable C library for dynamically generating PDF files. (License: Aladdin Free Public License)
- pdflib-devel
- Header file for pdflib. (License: Aladdin Free Public License)
Scientific/Cluster
- NCBI
- NCBI Toolkit. (License: GPL)
Scientific/Engineering
- NCBI-C++
- NCBI C++ Toolkit. (License: GPL)
- clustalx
- ClustalX. (License: GPL)
System Environment/Libraries
- fftw3
- Fast Fourier Transform library. (License: GPL)
- gd
- A graphics library for quick creation of PNG or JPEG images. (License: BSD-style)
- glut
- GL Utility Toolkit (GLUT). (License: Freely Redistributable)
Miscellaneous
- blt-scripts
- cups
- cups-common
- fonts-ttf-latex
- gcc-gfortran
- libgfortran0
- lyx
- rdate
- tetex-afm
- unrar (?)
- xdrawchem
- xxdiff
Molecular docking resources
- CureCancer Screensaver Lifesaver A large-scale distributed docking effort by Oxford University, NFCR and UnitedDevices, applying the LigandFit software, aimed to finding drugs for pancreatic cancer and leukemia.
- FIGHTAIDS@Home A project by The Scripps Institute, applying the AutoDock drug-docking software towards discovery of new HIV therapies
- Rosetta@Home A distributed computing project, aiming to improve the Rosetta software for protein prediction, design and docking
- ClusPro A docking program developed by the Camacho group at Boston University
- SmoothDock A docking prediction program and Online server by Prof. Carlos J. Camacho and Christoph Champ at University of Pittsburgh
- AutoDock A docking program developed by the Olson group at The Scripps Research Institute
- DOCK A docking program developed in the Kuntz and Shoichet groups at the University of California, San Francisco
- eHiTS A docking program developed by SimBioSys in Toronto, Canada
- GOLD A docking program produced by the CCDC in Cambridge, UK
- Glide A docking program developed and commercialized by Schrödinger in the US
- FlexX A docking program developed by BioSolveIT in Germany
- Molegro Virtual Docker A docking program developed by Molegro in Denmark
- ICM A docking program developed by Prof. Ruben Abagyan and Dr. Maxim Totrov at Molsoft LLC
