MALT statistics

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Citations per year

Citations chart

Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

MALT specifications


Unique identifier OMICS_18003
Alternative name MEGAN alignment tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Output format TXT, TAB, SAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Alexander Herbig <>

Additional information


Publication for MEGAN alignment tool

MALT in publications

PMCID: 5513282
PMID: 28705183
DOI: 10.1186/s13071-017-2279-1

[…] were employed for trimming for quality and length, removal of adaptor and background mapping [, ]. acquired reads were aligned to the refseq viral nucleotide and protein genome database using malt (megan alignment tool, v0.3.8) and diamond v0.7.1 tools [, ]. de novo assembly of the virus genomic segments were carried out using geneious software v9.1 (biomatters ltd., auckland, new zealand)., […]

PMCID: 5581243
PMID: 28460196
DOI: 10.1146/annurev-genom-091416-035526

[…] those that focus on specific groups of bacteria, such as enterobase ( and the homd (). pipelines that utilize whole-genome data for taxonomic assignments include the megan alignment tool (malt) () and midas ()., metagenomic tools differ not only in the way that their reference databases are constructed but also in the way those databases are queried, […]

PMCID: 5360070
PMID: 28320443
DOI: 10.1186/s13071-017-2087-7

[…] by the manufacturer. an illumina hiseq 1500 (illumina inc.) platform was used for the sequencing runs. reads were aligned to the refseq viral nucleotide and protein genome database using malt (megan alignment tool, v0.3.8) and diamond (v0.7.1) tools [, ]. de novo assembly of the full genome was carried out in geneious v9.1 (biomatters ltd, auckland, new zealand)., a total of 12,711 […]

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MALT institution(s)
Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany; Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Mummies and the Iceman, European Academy of Bozen/Bolzano (EURAC), Bolzano, Italy; Center for Bioinformatics, University of Tübingen, Tübingen, Germany
MALT funding source(s)
Supported by the European Research Council (ERC) starting grant APGREID; the South Tyrolian grant legge 14.

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