The article discusses the development and application of MEGAN4, an integrated platform for analyzing environmental sequence data. MEGAN4 addresses the challenge of integrating different types of data, including metagenomic, metatranscriptomic, metaproteomic, and rRNA data, to provide a unified approach to taxonomic and functional analysis. The program uses the NCBI taxonomy for taxonomic analysis and the SEED and KEGG classifications for functional analysis. MEGAN4 supports various data formats and can handle large datasets efficiently. The article includes examples of using MEGAN4 to analyze multiple data sets from marine studies, demonstrating its ability to integrate and compare different types of data. The program is freely available for academic purposes and can be downloaded from the authors' website.The article discusses the development and application of MEGAN4, an integrated platform for analyzing environmental sequence data. MEGAN4 addresses the challenge of integrating different types of data, including metagenomic, metatranscriptomic, metaproteomic, and rRNA data, to provide a unified approach to taxonomic and functional analysis. The program uses the NCBI taxonomy for taxonomic analysis and the SEED and KEGG classifications for functional analysis. MEGAN4 supports various data formats and can handle large datasets efficiently. The article includes examples of using MEGAN4 to analyze multiple data sets from marine studies, demonstrating its ability to integrate and compare different types of data. The program is freely available for academic purposes and can be downloaded from the authors' website.