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ASaturA specifications

Information


Unique identifier OMICS_24801
Name ASaturA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Additional information


http://bioinformatics.psb.ugent.be/downloads/psb/asatura/README.txt

Publication for ASaturA

ASaturA in pipeline

2013
PMCID: 3760282
PMID: 24002378
DOI: 10.1038/srep02468

[…] alignment based on direct visual inspection and using entropy-two (www.hiv.lanl.gov). this alignment was then refined using the geneious alignment software. amino-acid saturation was tested using asatura, and together with visual inspection this led to the removal of a significant number of sites including virtually all gap containing positions and their often ambiguously aligned neighboring […]


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ASaturA in publications

 (7)
PMCID: 4501334
PMID: 26175406
DOI: 10.7554/eLife.06974.033

[…] (). phylogenetic trees of all investigated enzymes were constructed using the ml approach (raxml []), bayesian inference (phylobayes []), and a method designed to deal with amino acid saturation (asatura []). ml trees were computed under the gamma corrected lg4x model of evolution as implemented in raxml 7.4.8a using the rapid-bootstrap optimization algorithm in 1000 replicates. bayesian […]

PMCID: 3760282
PMID: 24002378
DOI: 10.1038/srep02468

[…] alignment based on direct visual inspection and using entropy-two (www.hiv.lanl.gov). this alignment was then refined using the geneious alignment software. amino-acid saturation was tested using asatura, and together with visual inspection this led to the removal of a significant number of sites including virtually all gap containing positions and their often ambiguously aligned neighboring […]

PMCID: 3543385
PMID: 23088497
DOI: 10.1186/1750-2187-7-16

[…] were used to calculate p-values (heteroscedastic t-testing)., individual beta-propeller blade sequences of the wipi protein family were analysed phylogenetically using clans cluster analysis [] and asatura neighbor-joining phylogeny [] as previously described []., ampk: amp-activated protein kinase; atg: autophagy related; dmem: dulbecco's modified eagle medium; ebss: earl's balanced salt […]

PMCID: 2950852
PMID: 20949086
DOI: 10.1371/journal.pone.0013234

[…] topology only when the most sophisticated methods designed to deal with a compositional bias and long branch attraction phenomenon (lba) (phylobayes 3.2d-cat model; nh phylobayes 0.2.1-catbp model; asatura-lg model; see for details) were used. all other conventional analyses (nucleotide mp, ml and amino acid based mp, ml) either placed the diatom nuclear psb28 to the unsupported position […]

PMCID: 2660306
PMID: 19200367
DOI: 10.1186/1471-2148-9-34

[…] obtaining branch confidence values by bootstrapping with 1000 iterations. for nj and me analyses, the jtt model was used with a gamma distribution parameter estimated by phyml (α = 0.91). finally, asatura was used to remove saturated amino acid positions from the alignment prior to nj tree reconstruction [] using the jtt model., phylogenetic analysis was performed on seven vertebrate gene […]


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ASaturA institution(s)
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Gent University, Gent, Belgium; Department of Biology, Universitat Konstanz, Konstanz, Germany
ASaturA funding source(s)
Supported by the University of Konstanz and the German Science Foundation (DFG PE 842/21) and the National Sciences and Engineering Research Council of Canada for a Postdoctoral Fellowship.

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