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MEGAN6 Download Page. This is the official download site for the most recent version of MEGAN 6. The Community Edition of the paper is described here: Huson et al,, (2016), PLoS Computational Biology. Please post questions and bug reports to the community website.
- AnnoTree for Megan
MEGAN-AnnoTree Download Page This is the download site for...
- Megan6 Old Download Files
MEGAN6 Old Files Latest mapping files are here . Old mapping...
- User Manual for MEGAN V6.25
MEGAN is written in the programming language Java. The...
- AnnoTree for Megan
MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application. Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA. Functional analysis using InterPro2GO, SEED, eggNOG or KEGG.
Request a free trial & quote! MEGAN Metagenomics Analysis Software allows visual and quantitative exploration of microbiomes on a desktop computer. Your data is simultaneously annotated for taxonomic and functional composition to a wide range of databases.
- Contents
- 4 Program Overview
- 5 Importing, Reading and Writing Files
- 5.3 DAA Files
- 5.6 CSV Files
- 7 Taxonomic Binning
- 7.2 The NCBI-NR and NCBI-NT Databases
- 7.3 Assigning Reads to Taxa
- 8.5 Overriding MEGAN’s classification
- 9 Comparison of samples
- 10 Main Window
- 10.2 The Open Recent Submenu
- Export!Matches...
- 10.5 The Edit Menu
- 10.6 The Colors Submenu
- 10.7 The Preferences Submenu
- 10.8 The Accession Parsing Submenu
- 10.9 The Fix Taxon Mapping Submenu
- 10.10 The Preferences Disabling Submenu
- 10.11 The Select Menu
- Select!All Leaves
- 10.12 The Taxonomic Rank Submenu
- 10.13 The Options Menu
- Options!Change LCA Parameters...
- 10.14 The Layout Menu
- Layout!Phylogram
- 10.15 The Expand/Contract Submenu
- 10.16 The Tree Menu
- 10.17 The Collapse At Taxonomic Rank Submenu
- 10.18 The Window Menu
- Window!Correlation Plot...
- 10.19 Popup Menus
- 10.20 The Toolbar
- 10.21 The MEGAN Menu
- 10.22 Wheel Mouse and Special Keys
- 11 Sample Viewer
- 11.1 The Attributes Menu
- Attributes!Import From File...
- 11.2 The Samples Menu
- Samples!Open RMA File...
- 11.3 The Node Shape Submenu
- 11.4 The Algorithms Menu
- Algorithms!Extract Samples...
- 12 Cluster Analysis Viewer
- The Cluster Analysis Viewer Edit menu contains the following items:
- 12.2 The Cluster Analysis Node Shape Submenu
- The Cluster Analysis Viewer Select menu contains the following items:
- The Cluster Analysis Viewer Options menu contains the following items:
- The Cluster Analysis Viewer View menu contains the following items:
- 13 Import from Blast Dialog
- 13.1 Files Tab
- 13.4 eggNOG Tab
- 13.5 SEED Tab
- 13.6 KEGG Tab
- 13.7 LCA Parameters Tab
- 14 Inspector Window
- 14.1 Inspector Menus
- 14.2 The Inspector Edit Menu
- Edit!Show Reads...
- 14.3 The Inspector Options Menu
- 15 Rarefaction Window
- 15.1 The Rarefaction Window Edit Menu
- 15.2 The Rarefaction Window Options Menu
- 15.3 The Rarefaction Window Layout Menu
- 15.4 The Rarefaction Window Font Submenu
- 16 Chart Window
- 16.1 Taxon Chart Window
- 18 eggNOG Window
- 19 SEED Window
- 21 Extending Mapping Files
- 22 User-defined Classifications
- 23 Alignment Viewer
- 23.1 The Alignment Viewer Export Submenu
- Export!Overlap Graph...
- 23.2 The Alignment Viewer Edit Menu
- 23.3 The Alignment Viewer Preferences Submenu
- 23.4 The Alignment Viewer Options Menu
- Options!Matches Vs Reference
- Options!Matches Vs Consensus
- 24 Group Viewer
- 25 Find Toolbar
- • Use the Uncollapse...
- 26 Format Dialog
- 27 Message Window
- 28 Parameters Dialog
- 29 Compare Dialog
- 30 Extractor Dialog
- 31 Export Image Dialog
- 32 About Window
- 34.4 How MEGAN Parses Taxon Names
- 34.5 Required Format of Read Files
- 34.7 Tree and Map Format
- 36 Command-Line Commands
- 36.1 Writing Scripts
- 39 Acknowledgments
Contents Introduction Getting Started Obtaining and Installing the Program Program Overview Importing, Reading and Writing Files Long Reads Taxonomic Binning Functional Analysis Comparison of samples Main Window Sample Viewer Cluster Analysis Viewer Import from Blast Dialog Inspector Window Rarefaction Window Daniel H. Huson
In this section, we give an overview over the main design goals and features of this program. Basic knowl-edge of the underlying design of the program should make it easier to use the program. MEGAN is written in the programming language Java. The advantages of this is that we can provide versions that run under the Linux, MacOS, Windows and Unix o...
To open an existing RMA file or MEGAN file, select the File!Open... menu item and then browse to the desired file. Alternatively, if the file was recently opened by the program, then it may be contained in the File!Open Recent submenu. By default, when parsing an input file, for each read, taxon and RefSeq id, only one best-scoring match is kept. F...
MEGAN can parse files in DAA format [5]. Note, however, that DAA files usually do not contain the names of the taxa associated with the reference sequences and so one must supply suitable mapping files that map identifiers used for the reference sequences to NCBI taxa and functional classes, see below. In addition, the daa-meganizer program can be ...
MEGAN supports import of data from other programs in a delimiter-separated format (using comma’s or tabs) from a CSV file.
By default, MEGAN uses the NCBI taxonomy for taxonomic binning.
The NCBI-NR (“non-redundant”) protein sequence database is available from the NCBI website. It contains entries from GenPept, Swissprot, PIR, PDF, PDB and RefSeq. It is non-redundant in the sense that identical sequences are merged into a single entry. The NCBI-NT nucleotide sequence database is available from the NCBI website. It contains entries ...
The main problem addressed by MEGAN is to compute a “species profile” by assigning the reads from a metagenomics sequencing experiment to appropriate taxa in the NCBI taxonomy. At present, this program implements the following naive approach to this problem: Compare a given set of DNA reads to a database of known sequences, such as NCBI-NR or NCBI-...
You can override the assignments that MEGAN makes to functional classes as follows. Assume that you meganized DAA file (or RMA6, similarly) file is called microbiome.daa. To override MEGAN’s KEGG classification algorithm, say, provide a file called microbiome.kegg that is contained in the same direc-tory as the DAA file. The file suffix must match ...
Multiple samples can be opened simultaneously and then displayed together in a comparison view, by se-lecting the File!Compare... menu item. The samples are presented in a composite comparison document.
TheMain window is used to display the taxonomy and to control the program via the main menus. Initially, at startup, before reopening or creating a new RMA file, the Main window displays the NCBI taxonomy. By default, the taxonomy is only drawn to its third level. Parts of the taxonomy, or the full taxonomy, can be explored using the menu items of ...
The Open Recent menu allows the user to reopen recently opened files.
item: Export all matches to a text file (or only those for selected nodes, if any selected). The Export!Alignments... item: Calculate and export alignments for all selected leaves. The Export!Gene-Centric Assembly... assembly” of reads for all selected nodes. item: Compute and export a “gene-centric • The Export!MEGAN Summary File... item: Export a...
The Edit menu contains the following items: The Edit!Cut item: Cut. The Edit!Copy item: Copy. The Edit!Copy Image item: Copy image to clipboard. The Edit!Copy Legend item: Copy legend image to clipboard. The Edit!Paste item: Paste. The Edit!Edit Node Label item: Edit the node label. The Edit!Edit Edge Label item: Edit the edge label. The Edit!Descr...
The Colors menu contains a number of different color tables to choose from. In addition, the menu contains the following items: The Colors!Color By Labels item: each label is assigned a color from the chosen color table and this choice is maintained accross multiple windows and samples. The Colors!Color By Position item: items are colored according...
The Preferences menu contains the following items: • The Preferences!Show Notifications item: use this to turn off notifications e.g. when running MEGAN remotely. The Preferences!Accession Parsing submenu. The Preferences!Taxon Disabling submenu. The Preferences!Use Alternative Taxonomy... omy.tre and taxonomy.map files. item: Open alternative taxo...
The Accession Parsing menu contains the following items: The Acession Parsing!First Word Is Accession item: Set this if the first word in a reference sequence header line is an accession number without any prefix. NCBI is transitioning to this new format. The Acession Parsing!Set Accession Tags item: Use this to specify how accessions are identifie...
The Fix Taxon Mapping menu contains the following items: • The Fix Taxon Mapping!Add A Change... mapping for a given taxon. item: Change the taxon name to taxon id The Fix Taxon Mapping!List All Changes... item: List all changes. The Fix Taxon Mapping!Clear All Changes... item: Clear all changes.
The Taxon Disabling menu contains the following items: The Taxon Disabling!Enable All item: Enable all taxa. The Taxon Disabling!Disable... item: Disable all selected taxa or all named ones. The Taxon Disabling!Enable... item: Enable all selected taxa or all named ones. The Taxon Disabling!List Disabled... item: List all disabled taxa.
The Select menu contains the following items: The Select!All Nodes item: Select nodes. The Select!None item: Deselect all nodes. The Select!From Previous Window item: Select from previous window. The
item: Select all leaves (except Not Assigned, No Hits and Low Complexity). The Select!All Internal Nodes item: Select all internal nodes. The Select!All Intermediate Nodes item: Select all intermediate nodes. The Select!Subtree item: Select subtree. The Select!Leaves Below item: Select all leaves below currently selected nodes. The Select!Nodes Abo...
The Taxonomic Rank menu contains the following items: The Taxonomic Rank!Domain item: Select Domain. The Taxonomic Rank!Phylum item: Select Phylum. The Taxonomic Rank!Class item: Select Class. The Taxonomic Rank!Order item: Select Order. The Taxonomic Rank!Family item: Select Family. The Taxonomic Rank!Genus item: Select Genus. The Taxonomic Rank!S...
The Options menu contains the following items: • The
item: Rerun the LCA analysis with different parameters. The Options!Set Number Of Reads... item: Set the total number of reads in the analysis (will initiate recalculation of all classifications). The Options!Project Assignments To Rank... ments to a specific taxonomic rank, in a new document. item: Project all taxonomic assign- The Options!List Su...
The Layout menu contains the following items: The Layout!Show Legend item: Show horizontal or vertical legend, or hide. The Layout!Increase Font Size item: Set the font size. The Layout!Decrease Font Size item: Decrease the font size. The Layout!Expand/Contract submenu. The Layout!Layout Labels item: Layout labels. The Layout!Scale Nodes By Assigne...
item: Draw tree as phylogram with all leaves positioned as left as possible. The Layout!Use Magnifier item: Turn the magnifier on or off. The Layout!Draw Leaves Only item: Only draw leaves. The Layout!Highlight Differences submenu.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
This program uses a number of external Java libraries. The JARs and their licenses are contained in the jars directory. MEGAN is obfuscated using yguard. This manual was updated to MEGAN by Sina Beier.
MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. Daniel H. Huson, Sina Beier, Isabell Flade, Anna Gorska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh and Rewati Tappu. PLoS Computational Biology, 2016.
MEGAN7 Download Page. This is the beta-release download site for the most recent version of MEGAN 7. Both the program and the mapping files are under testing. MEGAN7 Community Edition installers. This is open source.
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Aug 11, 2021 · This is a tutorial for MEGAN6 - the world’s only software that allows interactive metagenomics data analysis.
- 61 min
- 5.3K
- Computomics GmbH
