MEGAN5 Download Page

This is the official download site for MEGAN5. Please send feed back to Daniel Huson on any problems that you encounter.

Note that MEGAN4 licenses will not work for MEGAN5.

A license for academic use of MEGAN5 is available here.
Non-academic users please contact Daniel Huson for a commercial license or a trial license.

Program installers:

MEGAN_macos_5_10_0.dmg (64-bit, MacOS X)
MEGAN_windows_5_10_0.exe (32-bit, Windows)
MEGAN_windows-x64_5_10_0.exe (64-bit, Windows)
MEGAN_unix_5_10_0.sh (64-bit, Linux, Unix)

Release notes
Manual md5sums

Auxiliary mapping files for taxon analysis:

If the BLAST or other comparison files do not contain taxon names, but do contain GI numbers, then load the following mapping file to allow MEGAN to determine taxon names. The file has to be unzipped before it can be used:
http://www-ab.informatik.uni-tuebingen.de/data/software/megan5/download/gi_taxid-March2015X.zip
This indexed file maps 659 million GI accession numbers to taxon ids. It will work with both DNA and protein alignments. It is based on the files "gi_taxid_nucl.dmp.gz" and "gi_taxid_prot.dmp.gz" that are available from NCBI and was extended by parsing by treating all GI numbers that appear together in the header line of some sequence in the NR database as equivialent. Non-indexed NCBI files will not work with MEGAN.

Auxiliary mapping files for KEGG analysis:

MEGAN uses a built-in RefSeq to KEGG mapping to determine the KO number of a given gene. The built-in ref-to-KEGG mapping file is out-of date and will not work well. If the BLAST or comparison files contain GI numbers, then load the following mapping file to allow MEGAN to determine KEGG KO assignments. The file has to be unzipped before it can be used:
http://www-ab.informatik.uni-tuebingen.de/data/software/megan5/download/gi2kegg.zip

Auxiliary mapping files for SEED analysis:

MEGAN uses a built-in RefSeq to SEED mapping to determine the functional role of a given gene. The built-in refseq-to-Seed mapping file is out-of date and will not work well. If the BLAST or comparison files contain GI numbers, then load the following mapping file to allow MEGAN to determine SEED functional groups:
http://www-ab.informatik.uni-tuebingen.de/data/software/megan5/download/gi2seed.map.gz

Updates of NCBI taxonomy:

To update to the latest NCBI taxonomy, download the following file:
http://www-ab2.informatik.uni-tuebingen.de/megan/taxonomy/ncbi.zip
In the installation directory of MEGAN, unzip the file in the class/resources/files directory.