Datamonkey is a web-based tool for detecting sites under positive or negative selection in codon alignments. It uses maximum likelihood-based methods, ranging from fast data exploration to complex models, and runs in parallel on a computer cluster. The tool provides a user-friendly interface for uploading alignments, performing phylogenetic analysis, and visualizing results. It implements three complementary methods: Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), and Random Effects Likelihood (REL). SLAC is efficient for large alignments, FEL is suitable for intermediate-sized datasets, and REL is the most powerful but may have higher Type I error rates. Datamonkey allows users to upload alignments in various formats, run BLAST searches, perform phylogenetic reconstruction, and select appropriate evolutionary models. It also detects adaptive and functionally constrained sites, offering faster and more statistically robust results than existing methods. The tool is accessible via a web interface and can be used for analyses up to 96 hours. Datamonkey is hosted on a Linux cluster and is designed to be self-contained, allowing users to run various analyses and visualize results. Future plans include distributing a complete package for installation on POSIX-compliant servers. The research was supported by several grants from the National Institutes of Health and other funding sources.Datamonkey is a web-based tool for detecting sites under positive or negative selection in codon alignments. It uses maximum likelihood-based methods, ranging from fast data exploration to complex models, and runs in parallel on a computer cluster. The tool provides a user-friendly interface for uploading alignments, performing phylogenetic analysis, and visualizing results. It implements three complementary methods: Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), and Random Effects Likelihood (REL). SLAC is efficient for large alignments, FEL is suitable for intermediate-sized datasets, and REL is the most powerful but may have higher Type I error rates. Datamonkey allows users to upload alignments in various formats, run BLAST searches, perform phylogenetic reconstruction, and select appropriate evolutionary models. It also detects adaptive and functionally constrained sites, offering faster and more statistically robust results than existing methods. The tool is accessible via a web interface and can be used for analyses up to 96 hours. Datamonkey is hosted on a Linux cluster and is designed to be self-contained, allowing users to run various analyses and visualize results. Future plans include distributing a complete package for installation on POSIX-compliant servers. The research was supported by several grants from the National Institutes of Health and other funding sources.