MALT statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MALT

Tool usage distribution map

This map represents all the scientific publications referring to MALT per scientific context
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Associated diseases

This word cloud represents MALT usage per disease context

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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




No version available


  • person_outline Alexander Herbig

Additional information


Publication for MEGAN alignment tool

MALT citations


Generic amplification and next generation sequencing reveal Crimean Congo hemorrhagic fever virus AP92 like strain and distinct tick phleboviruses in Anatolia, Turkey

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

[…] s 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). […]


A Robust Framework for Microbial Archaeology

Annu Rev Genomics Hum Genet
PMCID: 5581243
PMID: 28460196
DOI: 10.1146/annurev-genom-091416-035526

[…] o 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 (). […]


Co circulation of West Nile virus and distinct insect specific flaviviruses in Turkey

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

[…] gested 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). […]

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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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