├── TODO.md └── README.md /TODO.md: -------------------------------------------------------------------------------- 1 | # TO DO 2 | - Add the prices to each tool. 3 | - Specify if each tool is open source? 4 | - Add descriptions to each list entry. -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | *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 lance.lafontaine92@gmail.com and I'll accredit you for your suggestions. Thanks!* 2 | 3 | # Bioinformatics Tool List. 4 | 5 | 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! 6 | 7 | ### General-Purpose Resources and Databases. 8 | 9 | - [National Center for Biotechnology Information (NCBI)](http://www.ncbi.nlm.nih.gov/) (**Web**) 10 | - [ExPASy SIB Bioinformatics Resource Portal](http://www.expasy.org/) (**Web**) 11 | - [European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI)](http://www.ebi.ac.uk/) (**Web**) 12 | - [Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)](http://www.rcsb.org/pdb/home/home.do) (**Web**) 13 | - [BioPieces](https://code.google.com/p/biopieces/) (**OS X, Linux**) 14 | - [Internation Genetically-Engineered Machine (iGEM) Registry of Standard Biological Parts](http://parts.igem.org/Main_Page) (**Web**) 15 | 16 | ### Programming Libraries 17 | 18 | - [.NET BIO](http://bio.codeplex.com/) 19 | - [BioGo](https://github.com/biogo) 20 | - [BioJava](http://biojava.org/wiki/Main_Page) 21 | - [BioPerl](http://www.bioperl.org/wiki/Main_Page) 22 | - [BioPHP](http://biophp.org/) 23 | - [BioPython](http://biopython.org/wiki/Main_Page) 24 | - [BioRuby](http://bioruby.org/) 25 | - [BioSmallTalk](https://code.google.com/p/biosmalltalk/) 26 | - [SeqAn](http://www.seqan.de/) (**C++**) 27 | 28 | ### Sequence Alignment Search Tool. 29 | 30 | - [Basic Local Alignment Search Tool](http://blast.ncbi.nlm.nih.gov/Blast.cgi) (**Web**) 31 | - [Infernal: Inference of RNA Alignments](http://infernal.janelia.org/) (**Windows, OS X, Linux**) 32 | 33 | ### Vector Viewing, Editing and Annotating. 34 | 35 | - [Benchling](https://benchling.com/) (**Web**) 36 | - [j5 Vector Editor](http://j5.jbei.org/VectorEditor/VectorEditor.html) by the Joint BioEnergy Resource (**Web**) 37 | - [GENtle](https://gentle.synbiota.com/) by Synbiota (**Web**) 38 | - [SnapGene](http://www.snapgene.com/) (**Windows, OS X**) 39 | 40 | ### Single Sequence Editing and Analysis. 41 | 42 | - [OligoAnalyzer](http://www.idtdna.com/analyzer/applications/oligoanalyzer/Default.aspx) by Integrated DNA Technologies (IDT) (**Web**) 43 | - [fr33.net - Life Science Tools](http://www.fr33.net/index.php) (**Web**) 44 | - [OligoCalc](http://www.basic.northwestern.edu/biotools/OligoCalc.html) (**Web**) 45 | - [4peaks](http://nucleobytes.com/index.php/4peaks) (**OS X**) 46 | - [BamView](http://bamview.sourceforge.net/) (**Web, Windows, OS X, Linux**) 47 | 48 | ### Multiple Sequence Alignment. 49 | 50 | - [T-Coffee](http://tcoffee.crg.cat/apps/tcoffee/index.html) (**Web**) 51 | - [MUSCLE](http://www.ebi.ac.uk/Tools/msa/muscle/) (**Web**) 52 | - [Clustal Omega](https://www.ebi.ac.uk/Tools/msa/clustalo/) (**Web**) 53 | - [Multalin](http://multalin.toulouse.inra.fr/multalin/) (**Web**) 54 | - [Molecular Evolutionary Genetics Analysis (MEGA)](http://www.megasoftware.net/) (**Windows and OS X**) 55 | 56 | ### Phylogenetic Analysis. 57 | 58 | - [Molecular Evolutionary Genetics Analysis (MEGA)](http://www.megasoftware.net/) (**Windows and OS X**) 59 | 60 | ### Gene Identification, Genome Assembly, Comparative Genomics. 61 | 62 | - [GLIMMER](http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi) by NCBI (**Web**) 63 | - [AMOS](http://sourceforge.net/projects/amos/) (**Windows, Linux**) 64 | - [BLAST Ring Image Generator (BRIG)](http://www.ncbi.nlm.nih.gov/pubmed/21824423) (**Windows, OS X, Linux**) 65 | - [Circos](http://circos.ca/) (**Windows, OS X, Linux**) 66 | - [Cortex](http://cortexassembler.sourceforge.net/index.html) (**C**) 67 | - [The CLEVER Toolkit](https://code.google.com/p/clever-sv/) (**C++ and Python**) 68 | - [EasyFig](http://easyfig.sourceforge.net/) (**Python Library**) 69 | 70 | 71 | ### Analysis of Protein Functional Domains. 72 | 73 | - [InterPro](http://www.ebi.ac.uk/interpro/) and [InterProScan5](http://www.ebi.ac.uk/Tools/pfa/iprscan5/) (**Web**) 74 | 75 | ### 2D RNA Molecular Structure Modelling. 76 | 77 | - [Mfold](http://mfold.rna.albany.edu/?q=mfold) (**Web**) 78 | - [UNAFold](http://mfold.rna.albany.edu/?q=unafold-man-pages) (**Web**) 79 | - [Quickfold](http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold) (**Web**) 80 | - [MC-FOLD](http://www.major.iric.ca/MC-Fold/) (**Web**) 81 | - [alteRNA](http://compbio.cs.sfu.ca/nwp-content/software/taverna/alterna/) (**Web**) 82 | - [inteRNA](http://compbio.cs.sfu.ca/nwp-content/software/taverna/interna/) (**Web**) 83 | - [CONTRAfold](http://contra.stanford.edu/contrafold/) (**Web, C++**) 84 | - [RNAstructure](http://rna.urmc.rochester.edu/rnastructure.html) (**Windows, OS X, Linux**) 85 | - [ViennaRNA](http://www.tbi.univie.ac.at/RNA/) (**Windows, OS X, Linux**) 86 | - [vsfold4](http://www.rna.it-chiba.ac.jp/~vsfold/vsfold4/) (**Web**) 87 | 88 | ### 3D Protein Molecular Structure Modelling. 89 | 90 | - [PyMoL](http://pymol.org/pymol) (**Windows, OS X, Linux**) 91 | - [BioBlender](http://www.bioblender.eu/) (**Windows, OS X, Linux**) 92 | - [FirstGlance in JMol](http://bioinformatics.org/firstglance/fgij/) (**Web**) 93 | - [RasMol](http://www.rasmol.org/) (**Windows, Linux**) 94 | 95 | ### Protein Structure Prediction 96 | 97 | - [SWISS-MODEL](http://swissmodel.expasy.org/?pid=smh01) (**Web**) 98 | - [SWISS-PDBViewer](http://spdbv.vital-it.ch/) 99 | - [Protein Structure Prediction Center](http://predictioncenter.org/) (**Web**) 100 | 101 | ### Mass Spectrometry Software 102 | 103 | - [MS-FIT](http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msfitstandard) (**Web**) 104 | 105 | ### Short Read Sequence Typing 106 | - [SRST2](https://katholt.github.io/srst2/) 107 | 108 | ### Learning Resources. 109 | 110 | - [Rosalind](http://rosalind.info/problems/locations/) (**Web**) 111 | 112 | ### Question and Answer (Q&A) Websites. 113 | 114 | - [Biostars: Bioinformatics Explained](https://www.biostars.org/) (**Web**) 115 | - [StackExchange Biology Beta](http://biology.stackexchange.com/) (**Web**) 116 | 117 | # Disclaimer 118 | 119 | I do not own or am not affiliated with any of these products, projects, services, companies, institutes or organizations referenced in this list. 120 | --------------------------------------------------------------------------------