MALIGN specifications


Unique identifier OMICS_26320
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A nucleic acids file and an amino acid sequences file.
Input format GenBank
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.7
Stability Stable
Source code URL
Maintained No


No version available



This tool is not maintained anymore.

Publication for MALIGN

MALIGN citations


SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)

PLoS One
PMCID: 3458043
PMID: 23049744
DOI: 10.1371/journal.pone.0044112
call_split See protocol

[…] esirable sequences such as those matching non-cellular and rRNA sequences. Once identified, those sequences were removed from the final set of processed ESTs. For clustering, ESTs were evaluated with malign, a k-mer-based alignment tool , which clusters ESTs based on sequence overlap (k-mer  = 16, seed length requirement  = 32, alignment identity > = 98%). Clusters of ESTs were further merged base […]


Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae maydis identify novel genes expressed during vegetative, infectious, and reproductive growth

BMC Genomics
PMCID: 2596140
PMID: 18983654
DOI: 10.1186/1471-2164-9-523
call_split See protocol

[…] ared against the GenBank nucleotide database by BLAST [] to identify contaminants; undesirable ESTs such as those matching non-cellular sequences were removed.For clustering, ESTs were evaluated with MALIGN [], a kmer-based alignment tool that clusters ESTs based on sequence overlap (kmer = 16, seed length requirement = 32, alignment ID >= 98%). Clusters of ESTs were further merged based on sister […]

MALIGN institution(s)
Department of Invertebrates, American Museum of Natural History, New York, NY, USA

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