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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 citations

 (9)
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Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement

2016
PLoS One
PMCID: 5115734
PMID: 27861576
DOI: 10.1371/journal.pone.0166338
call_split See protocol

[…] ved in SeaView []. Phylogenetic trees were constructed using Maximum Likelihood (RAxML v8.2.4; []), Bayesian inference (PHYLOBAYES v3.3b; []) and a method designed to deal with amino acid saturation (AsaturA v18.10.2002; []). ML trees were computed using the LG model with gamma distribution in 4 categories and 1000 replicates. Bayesian inferences were calculated with the following parameters: 2 ch […]

library_books

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

2015
eLife
PMCID: 4501334
PMID: 26175406
DOI: 10.7554/eLife.06974.033

[…] can (). 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 phylo […]

library_books

Complete mitochondrial genomes of the human follicle mites Demodex brevis and D. folliculorum: novel gene arrangement, truncated tRNA genes, and ancient divergence between species

2014
BMC Genomics
PMCID: 4320518
PMID: 25515815
DOI: 10.1186/1471-2164-15-1124

[…] urate much more rapidly than protein sequences (20 possible amino acids). Furthermore, to assess whether there was substantial saturation among the amino acid substitutions, we also used the software AsaturA [] to visualize the accumulation of amino acid substitutions with genetic distance, which showed that there was only very slight saturation of even the most frequent types of amino acid substi […]

library_books

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

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

[…] ity 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 p […]

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Defining regulatory and phosphoinositide binding sites in the human WIPI 1 β propeller responsible for autophagosomal membrane localization downstream of mTORC1 inhibition

2012
PMCID: 3543385
PMID: 23088497
DOI: 10.1186/1750-2187-7-16
call_split See protocol

[…] 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 []. […]

call_split

A Gene in the Process of Endosymbiotic Transfer

2010
PLoS One
PMCID: 2950852
PMID: 20949086
DOI: 10.1371/journal.pone.0013234
call_split See protocol

[…] el) . Because the third codon position appeared to be saturated, we excluded this position prior to the analysis (trees not shown). Amino acid alignments were used to construct MP , Neighbor joining (AsaturA ; method designed to deal with saturation of amino acids with LG model ); Bayesian (CAT-BP model as implemented in NH PhyloBayes 0.2.1 ; CAT model in PhyloBayes 3.2d ) and ML trees using PhyML […]

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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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