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Protocols

MALIGN specifications

Information


Unique identifier OMICS_26320
Name MALIGN
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 https://www.amnh.org/content/download/61087/1019190/version/1/file/malign.tar.gz
Maintained No

Versioning


No version available

Documentation


Maintainer


This tool is not maintained anymore.

Publication for MALIGN

MALIGN citations

 (2)
call_split

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

2012
PLoS One
PMCID: 3458043
PMID: 23049744
DOI: 10.1371/journal.pone.0044112
call_split See protocol

[…] 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 […]

library_books

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

2008
BMC Genomics
PMCID: 2596140
PMID: 18983654
DOI: 10.1186/1471-2164-9-523

[…] 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 […]


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

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