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https://github.com/lancelafontaine/bioinformatics-compbio-tools

A curated list of useful bioinformatics and computational biology tools, sorted by category.
https://github.com/lancelafontaine/bioinformatics-compbio-tools

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A curated list of useful bioinformatics and computational biology tools, sorted by category.

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*This list is far from being complete. If you have any software suggestions, fork this list and submit a pull request, or email me at [email protected] and I'll accredit you for your suggestions. Thanks!*



# Bioinformatics Tool List.



This repository contains a list of great bioinformatics and computational biology tools. These web and desktop programs are all free unless indicated otherwise, and are sorted by category. Please contribute by forking this list!



### General-Purpose Resources and Databases.



- [National Center for Biotechnology Information (NCBI)](http://www.ncbi.nlm.nih.gov/) (**Web**)

- [ExPASy SIB Bioinformatics Resource Portal](http://www.expasy.org/) (**Web**)

- [European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI)](http://www.ebi.ac.uk/) (**Web**)

- [Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)](http://www.rcsb.org/pdb/home/home.do) (**Web**)

- [BioPieces](https://code.google.com/p/biopieces/) (**OS X, Linux**)

- [Internation Genetically-Engineered Machine (iGEM) Registry of Standard Biological Parts](http://parts.igem.org/Main_Page) (**Web**)



### Programming Libraries



- [.NET BIO](http://bio.codeplex.com/)

- [BioGo](https://github.com/biogo)

- [BioJava](http://biojava.org/wiki/Main_Page)

- [BioPerl](http://www.bioperl.org/wiki/Main_Page)

- [BioPHP](http://biophp.org/)

- [BioPython](http://biopython.org/wiki/Main_Page)

- [BioRuby](http://bioruby.org/)

- [BioSmallTalk](https://code.google.com/p/biosmalltalk/)

- [SeqAn](http://www.seqan.de/) (**C++**)



### Sequence Alignment Search Tool.



- [Basic Local Alignment Search Tool](http://blast.ncbi.nlm.nih.gov/Blast.cgi) (**Web**)

- [Infernal: Inference of RNA Alignments](http://infernal.janelia.org/) (**Windows, OS X, Linux**)



### Vector Viewing, Editing and Annotating.



- [Benchling](https://benchling.com/) (**Web**)

- [j5 Vector Editor](http://j5.jbei.org/VectorEditor/VectorEditor.html) by the Joint BioEnergy Resource (**Web**)

- [GENtle](https://gentle.synbiota.com/) by Synbiota (**Web**)

- [SnapGene](http://www.snapgene.com/) (**Windows, OS X**)



### Single Sequence Editing and Analysis.



- [OligoAnalyzer](http://www.idtdna.com/analyzer/applications/oligoanalyzer/Default.aspx) by Integrated DNA Technologies (IDT) (**Web**)

- [fr33.net - Life Science Tools](http://www.fr33.net/index.php) (**Web**)

- [OligoCalc](http://www.basic.northwestern.edu/biotools/OligoCalc.html) (**Web**)

- [4peaks](http://nucleobytes.com/index.php/4peaks) (**OS X**)

- [BamView](http://bamview.sourceforge.net/) (**Web, Windows, OS X, Linux**)



### Multiple Sequence Alignment.



- [T-Coffee](http://tcoffee.crg.cat/apps/tcoffee/index.html) (**Web**)

- [MUSCLE](http://www.ebi.ac.uk/Tools/msa/muscle/) (**Web**)

- [Clustal Omega](https://www.ebi.ac.uk/Tools/msa/clustalo/) (**Web**)

- [Multalin](http://multalin.toulouse.inra.fr/multalin/) (**Web**)

- [Molecular Evolutionary Genetics Analysis (MEGA)](http://www.megasoftware.net/) (**Windows and OS X**)



### Phylogenetic Analysis.



- [Molecular Evolutionary Genetics Analysis (MEGA)](http://www.megasoftware.net/) (**Windows and OS X**)



### Gene Identification, Genome Assembly, Comparative Genomics.



- [GLIMMER](http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi) by NCBI (**Web**)

- [AMOS](http://sourceforge.net/projects/amos/) (**Windows, Linux**)

- [BLAST Ring Image Generator (BRIG)](http://www.ncbi.nlm.nih.gov/pubmed/21824423) (**Windows, OS X, Linux**)

- [Circos](http://circos.ca/) (**Windows, OS X, Linux**)

- [Cortex](http://cortexassembler.sourceforge.net/index.html) (**C**)

- [The CLEVER Toolkit](https://code.google.com/p/clever-sv/) (**C++ and Python**)

- [EasyFig](http://easyfig.sourceforge.net/) (**Python Library**)



### Analysis of Protein Functional Domains.



- [InterPro](http://www.ebi.ac.uk/interpro/) and [InterProScan5](http://www.ebi.ac.uk/Tools/pfa/iprscan5/) (**Web**)



### 2D RNA Molecular Structure Modelling.



- [Mfold](http://mfold.rna.albany.edu/?q=mfold) (**Web**)

- [UNAFold](http://mfold.rna.albany.edu/?q=unafold-man-pages) (**Web**)

- [Quickfold](http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold) (**Web**)

- [MC-FOLD](http://www.major.iric.ca/MC-Fold/) (**Web**)

- [alteRNA](http://compbio.cs.sfu.ca/nwp-content/software/taverna/alterna/) (**Web**)

- [inteRNA](http://compbio.cs.sfu.ca/nwp-content/software/taverna/interna/) (**Web**)

- [CONTRAfold](http://contra.stanford.edu/contrafold/) (**Web, C++**)

- [RNAstructure](http://rna.urmc.rochester.edu/rnastructure.html) (**Windows, OS X, Linux**)

- [ViennaRNA](http://www.tbi.univie.ac.at/RNA/) (**Windows, OS X, Linux**)

- [vsfold4](http://www.rna.it-chiba.ac.jp/~vsfold/vsfold4/) (**Web**)



### 3D Protein Molecular Structure Modelling.



- [PyMoL](http://pymol.org/pymol) (**Windows, OS X, Linux**)

- [BioBlender](http://www.bioblender.eu/) (**Windows, OS X, Linux**)

- [FirstGlance in JMol](http://bioinformatics.org/firstglance/fgij/) (**Web**)

- [RasMol](http://www.rasmol.org/) (**Windows, Linux**)



### Protein Structure Prediction



- [SWISS-MODEL](http://swissmodel.expasy.org/?pid=smh01) (**Web**)

- [SWISS-PDBViewer](http://spdbv.vital-it.ch/)

- [Protein Structure Prediction Center](http://predictioncenter.org/) (**Web**)



### Mass Spectrometry Software



- [MS-FIT](http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msfitstandard) (**Web**)



### Short Read Sequence Typing

- [SRST2](https://katholt.github.io/srst2/)



### Learning Resources.



- [Rosalind](http://rosalind.info/problems/locations/) (**Web**)



### Question and Answer (Q&A) Websites.



- [Biostars: Bioinformatics Explained](https://www.biostars.org/) (**Web**)

- [StackExchange Biology Beta](http://biology.stackexchange.com/) (**Web**)



# Disclaimer



I do not own or am not affiliated with any of these products, projects, services, companies, institutes or organizations referenced in this list.