A Practical Bioinformatician's Basic Toolkit

• ProfileGrid -  A new visual representation of large multiple sequence alignments
• Galaxy - A platform for large-scale, semi-automated, interactive analyses
  
• Jalview - Java Alignment Editor
  
• Artemis v9 - Free Genome Viewer And Annotation Tool (when saving the file, save as ".jar" instead of ".zip")
• BioEdit v7.0.9 - Free Sequence Alignment Editor
• ClustalX 2.0.9 - Free Multiple Sequence Alignment Program
• Muscle 3.6 - Free Multiple Sequence Alignment Software
• Promals - PROfile Multiple Alignment with Local Structure
• RASCAL - rapid scanning and correction of multiple sequence alignments
  
• ICM Molsoft v3.6 - Free 3D Molecular Graphics Software
• PyMol - Free Molecular Visualization System
• Rastop - Molecular Visualization Software
  
• Rasmol v2.7.3.1 - Free Molecular Visualization Software
• Modeller - Free 3D Modelling Software
• Beast - Free, cross-platform program for Bayesian MCMC analysis of molecular sequence phylogenetics (cool and powerful!)
  
• MEGA 4 - Free Molecular Evolutionary Genetics Analysis Software
• Phylip 3.68 - Free Phylogeny Inference Package
• TreeView - Free Phylogenetic Tree Drawing Software
• LAPIS - Free, Powerful And Easy To Use Text Manipulation Tool
• Jdotter - Java Dot Plot Alignments
  
• Dotter - A graphical dotplot program Tutorial 1 Tutorial 2