MEGAN4 is an updated version of the MEGAN program designed for the integrative analysis of environmental sequence data, including metagenomic, metatranscriptomic, metaproteomic, and rRNA data. It provides a unified approach to both taxonomic and functional analysis, using the NCBI taxonomy for taxonomic classification and the SEED or KEGG classifications for functional analysis. MEGAN4 allows users to import and compare classification results from other tools, and it is freely available for academic use. The program supports multiple operating systems and is fully multithreaded, enabling efficient processing of large datasets. MEGAN4 uses a homology-based approach, comparing sequencing reads against reference databases such as NCBI-NR and SILVA. It also supports machine-learning methods for classification. The program can analyze amplicon data targeting rRNA by comparing sequences against the SILVA database. MEGAN4 allows users to perform interactive analysis, view taxonomic and functional results, and extract specific reads for further study. The program is particularly useful for comparing different types of environmental data, such as metagenomes, metatranscriptomes, and metaproteomes. It provides visualizations of taxonomic and functional content, enabling researchers to explore data at different levels of detail. MEGAN4 also supports the analysis of large datasets by partitioning reads and BLAST results across multiple files. In comparison with other tools, MEGAN4 offers accurate and efficient analysis of taxonomic and functional content. It can be used to compare data sets from different sources and environments, such as marine samples, and to identify correlations between environmental parameters and microbial composition. MEGAN4 is also compatible with various reference databases and can be extended to support new data types and analysis methods. MEGAN4 is an interactive and user-friendly tool that facilitates the integrative analysis of environmental sequence data. It enables researchers to explore complex microbial communities and understand their functional roles in different environments. The program is continuously being improved to support new technologies and data types, ensuring its relevance in the rapidly evolving field of metagenomics.MEGAN4 is an updated version of the MEGAN program designed for the integrative analysis of environmental sequence data, including metagenomic, metatranscriptomic, metaproteomic, and rRNA data. It provides a unified approach to both taxonomic and functional analysis, using the NCBI taxonomy for taxonomic classification and the SEED or KEGG classifications for functional analysis. MEGAN4 allows users to import and compare classification results from other tools, and it is freely available for academic use. The program supports multiple operating systems and is fully multithreaded, enabling efficient processing of large datasets. MEGAN4 uses a homology-based approach, comparing sequencing reads against reference databases such as NCBI-NR and SILVA. It also supports machine-learning methods for classification. The program can analyze amplicon data targeting rRNA by comparing sequences against the SILVA database. MEGAN4 allows users to perform interactive analysis, view taxonomic and functional results, and extract specific reads for further study. The program is particularly useful for comparing different types of environmental data, such as metagenomes, metatranscriptomes, and metaproteomes. It provides visualizations of taxonomic and functional content, enabling researchers to explore data at different levels of detail. MEGAN4 also supports the analysis of large datasets by partitioning reads and BLAST results across multiple files. In comparison with other tools, MEGAN4 offers accurate and efficient analysis of taxonomic and functional content. It can be used to compare data sets from different sources and environments, such as marine samples, and to identify correlations between environmental parameters and microbial composition. MEGAN4 is also compatible with various reference databases and can be extended to support new data types and analysis methods. MEGAN4 is an interactive and user-friendly tool that facilitates the integrative analysis of environmental sequence data. It enables researchers to explore complex microbial communities and understand their functional roles in different environments. The program is continuously being improved to support new technologies and data types, ensuring its relevance in the rapidly evolving field of metagenomics.