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GramAlign specifications

Information


Unique identifier OMICS_05314
Name GramAlign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline GramAlign Team

Information


Unique identifier OMICS_05314
Name GramAlign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline GramAlign Team

Publication for GramAlign

GramAlign citations

 (3)
library_books

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

2016
PLoS Biol
PMCID: 5115861
PMID: 27861590
DOI: 10.1371/journal.pbio.2000225

[…] d for a minimum group size of two counts, with dereplication based on full sequences []. Representative sequences were chosen as the most abundant representative in each OTU cluster and aligned using GramAlign []. A phylogenetic tree of the representative sequences was built in QIIME [] with the FastTree method and midpoint rooting []. Taxonomy was then assigned to the OTU representatives with the […]

library_books

ReformAlign: improved multiple sequence alignments using a profile based meta alignment approach

2014
BMC Bioinformatics
PMCID: 4133627
PMID: 25099134
DOI: 10.1186/1471-2105-15-265

[…] We assessed the effect ReformAlign on the deriving alignments of ten leading methods: ClustalW [], ClustalO [], MUSCLE [, ], MAFFT [], Kalign [], GramAlign [], ProbConsRNA [], R-Coffee [, ], PicXAA [] and Dialign-TX []. These aligners implement a variety of alignment techniques, such as progressive alignment [, , ], iterative refinement [, , ], […]

library_books

Protein multiple sequence alignment by hybrid bio inspired algorithms

2010
Nucleic Acids Res
PMCID: 3064771
PMID: 21071394
DOI: 10.1093/nar/gkq1052

[…] BASE v.3.0 benchmark. Also in this new testbed, IMSA shows good alignments, which are comparable with the state-of-the-art methods, as MUSCLE (fast), MAFFT (fast), MAFFT v6 (parttree, nā€‰=ā€‰50), MAFFT, GramAlign, Kalign, ClustalW (fast), MUSCLE, ClustalW, PSAlign, and T-Coffee. […]

Citations

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GramAlign institution(s)
Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA

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