Why should you use a review tool? There are a few reasons: 1. Review can find many faults during requirements, design and coding; 2. Early detection of errors can improve productivity; 3. Review helps members of the team learn about other parts of the system, and can increase their overall programming skill.

PMD scans Java source code and looks for potential problems like: * Possible bugs - empty try/catch/finally/switch statements * Dead code - unused local variables, parameters and private methods * Suboptimal code - wasteful String/StringBuffer usage * Overcomplicated expressions - unnecessary if statements, for loops that could be while loops * Duplicate code - copied/pasted code means copied/pasted bugs

Checkstyle is a development tool to help programmers write Java code that adheres to a coding standard. It automates the process of checking Java code to spare humans of this boring (but important) task. This makes it ideal for projects that want to enforce a coding standard.

BACKGROUND: Many RNA viruses do not have a single, representative genome but instead form a set of related variants that has been called a quasispecies. The sequence variability of such viruses presents a significant bioinformatics challenge. In order for the sequence information to be understood, the complete mutational spectrum needs to be distilled to a biologically relevant and analyzable representation. RESULTS: Here, we develop a "selection mapping" algorithm?QUASI?that identifies the positively selected variants of viral proteins. The key to the selection mapping algorithm is the identification of particular replacement mutations that are overabundant relative to silent mutations at each codon (e.g., threonine at hemagglutinin position 262). Selection mapping identifies such replacement mutations as positively selected. Conversely, selection mapping recognizes negatively selected variants as mutational "noise" (e.g., serine at hemagglutinin position 262). CONCLUSION: Selection mapping is a fundamental improvement over earlier methods (e.g., dN/dS) that identify positive selection at codons but do not identify which amino acids at these codons confer selective advantage. Using QUASI?s selection maps, we characterize the selected mutational landscapes of influenza A H3 hemagglutinin, HIV-1 reverse transcriptase, and HIV-1 gp120.