The Molecular Evolutionary Genetics Analysis (MEGA) software has been updated to version 11, introducing significant enhancements for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Key additions include: 1. **Relaxed-Clock Dating Facilities**: New methods for node-dating and tip-dating are implemented, allowing for more accurate divergence time estimation. The software supports the use of probability densities for calibration constraints, enhancing the precision of divergence time estimates. 2. **Bayesian Method for Neutral Evolutionary Probabilities**: A Bayesian method is added to estimate neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments, aiding in the diagnosis of disease mutations and detecting adaptive variants. 3. **Machine Learning for Autocorrelation Detection**: A machine learning method is included to test for autocorrelation of evolutionary rates in phylogenies, which is crucial for understanding molecular evolution patterns. 4. **Memory-Efficient Maximum Likelihood Analyses**: The software has been refactored to reduce memory requirements for maximum likelihood analyses, making it feasible to analyze larger data sets. 5. **Enhanced GUI for Large Data Sets**: The graphical user interface (GUI) has been improved to be more responsive and interactive, particularly for very large data sets. Background threads are used to handle long-running operations, and the Tree Explorer has been extensively revamped to provide better visualization and customization options. These enhancements aim to improve the user experience, the quality of results, and the pace of biological discovery. MEGA11 is available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.The Molecular Evolutionary Genetics Analysis (MEGA) software has been updated to version 11, introducing significant enhancements for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Key additions include: 1. **Relaxed-Clock Dating Facilities**: New methods for node-dating and tip-dating are implemented, allowing for more accurate divergence time estimation. The software supports the use of probability densities for calibration constraints, enhancing the precision of divergence time estimates. 2. **Bayesian Method for Neutral Evolutionary Probabilities**: A Bayesian method is added to estimate neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments, aiding in the diagnosis of disease mutations and detecting adaptive variants. 3. **Machine Learning for Autocorrelation Detection**: A machine learning method is included to test for autocorrelation of evolutionary rates in phylogenies, which is crucial for understanding molecular evolution patterns. 4. **Memory-Efficient Maximum Likelihood Analyses**: The software has been refactored to reduce memory requirements for maximum likelihood analyses, making it feasible to analyze larger data sets. 5. **Enhanced GUI for Large Data Sets**: The graphical user interface (GUI) has been improved to be more responsive and interactive, particularly for very large data sets. Background threads are used to handle long-running operations, and the Tree Explorer has been extensively revamped to provide better visualization and customization options. These enhancements aim to improve the user experience, the quality of results, and the pace of biological discovery. MEGA11 is available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.