A Practical Bioinformatician's Advance Toolkit

• Mobyle - An integrated portal for diverse type of sophisticated bioinformatics analyses (highly recommended)
• PEMer - Construct and analyze structural variants
• BLASTZ - Multiple sequence alignment program for the whole-genome human-mouse alignments
• Polyphen - Prediction of Functional Effect of Human nsSNPs
  
• SIFT - Sorting Intolerant from Tolerant
  
• SNP3D - Assigns Molecular Functional Effects of Non-Synonymous SNPs Based on Structure and Sequence Analysis
• PLINK - a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
• PANTHER - Classifies Genes by Their Functions
• iTOL - Interactive Tree of Life
• iPATH - Interactive Pathways Explorer
  
• VisANT - Integrative Visual Analysis Tool for Biological Networks and Pathways
• STITCH - Interaction of networks of chemicals and proteins
• STRING - Proteins and their interactions
• Ka/Ks Calculation tool
• Sirius - An Extensible Molecular Graphics and Analysis Environment
• Local Blast Client - Run blast locally on your computer and on your custom defined dataset
  
• CD-HI/CD-HIT - Clustering tool to identify representative sequences
  
• R Bioconductor - A language and environment for statistical computing and graphics
• R Bioconductor with user-friendly point & click menu
• Gene Pattern - A powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks
• Pebl - Python Environment For Bayesian Learning
• Cytoscape - For visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
• Graphviz - Representing structural information as diagrams of abstract graphs and networks
• Weka - A collection of machine learning algorithms for data mining tasks
• HMMEditor - A visual editor for profile Hidden Markov Model (pHMM)