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!

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) (Web)
• ExPASy SIB Bioinformatics Resource Portal (Web)
• European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) (Web)
• Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (Web)
• BioPieces (OS X, Linux)
• Internation Genetically-Engineered Machine (iGEM) Registry of Standard Biological Parts (Web)

Programming Libraries

• .NET BIO
• BioGo
• BioJava
• BioPerl
• BioPHP
• BioPython
• BioRuby
• BioSmallTalk
• SeqAn (C++)

Sequence Alignment Search Tool.

• Basic Local Alignment Search Tool (Web)
• Infernal: Inference of RNA Alignments (Windows, OS X, Linux)

Vector Viewing, Editing and Annotating.

• Benchling (Web)
• j5 Vector Editor by the Joint BioEnergy Resource (Web)
• GENtle by Synbiota (Web)
• SnapGene (Windows, OS X)

Single Sequence Editing and Analysis.

• OligoAnalyzer by Integrated DNA Technologies (IDT) (Web)
• fr33.net - Life Science Tools (Web)
• OligoCalc (Web)
• 4peaks (OS X)
• BamView (Web, Windows, OS X, Linux)

Multiple Sequence Alignment.

• T-Coffee (Web)
• MUSCLE (Web)
• Clustal Omega (Web)
• Multalin (Web)
• Molecular Evolutionary Genetics Analysis (MEGA) (Windows and OS X)

Phylogenetic Analysis.

• Molecular Evolutionary Genetics Analysis (MEGA) (Windows and OS X)

Gene Identification, Genome Assembly, Comparative Genomics.

• GLIMMER by NCBI (Web)
• AMOS (Windows, Linux)
• BLAST Ring Image Generator (BRIG) (Windows, OS X, Linux)
• Circos (Windows, OS X, Linux)
• Cortex (C)
• The CLEVER Toolkit (C++ and Python)
• EasyFig (Python Library)

Analysis of Protein Functional Domains.

• InterPro and InterProScan5 (Web)

2D RNA Molecular Structure Modelling.

• Mfold (Web)
• UNAFold (Web)
• Quickfold (Web)
• MC-FOLD (Web)
• alteRNA (Web)
• inteRNA (Web)
• CONTRAfold (Web, C++)
• RNAstructure (Windows, OS X, Linux)
• ViennaRNA (Windows, OS X, Linux)
• vsfold4 (Web)

3D Protein Molecular Structure Modelling.

• PyMoL (Windows, OS X, Linux)
• BioBlender (Windows, OS X, Linux)
• FirstGlance in JMol (Web)
• RasMol (Windows, Linux)

Protein Structure Prediction

• SWISS-MODEL (Web)
• SWISS-PDBViewer
• Protein Structure Prediction Center (Web)

Mass Spectrometry Software

• MS-FIT (Web)

Short Read Sequence Typing

• SRST2

Learning Resources.

• Rosalind (Web)

Question and Answer (Q&A) Websites.

• Biostars: Bioinformatics Explained (Web)
• StackExchange Biology Beta (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.