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ATGC specifications

Information


Unique identifier OMICS_03173
Name ATGC
Alternative name Alignable Tight Genomic Clusters
Restrictions to use None
Maintained Yes

Publication for Alignable Tight Genomic Clusters

ATGC citations

 (315)
library_books

Ceftazidime Is the Key Diversification and Selection Driver of VIM Type Carbapenemases

2018
MBio
PMCID: 5941070
PMID: 29739906
DOI: 10.1128/mBio.02109-17

[…] or the phylogenetic analysis are listed in (last time accessed July 2017). The programs used to perform the phylogenetic analysis were the following: https://www.megasoftware.net/ (MEGA), http://www.atgc-montpellier.fr/phyml/ (PhyML), https://github.com/ddarriba/jmodeltest2 (jModeltest), http://darwin.uvigo.es/rdp/rdp.html (RDP), http://tree.bio.ed.ac.uk/software/ (BEAST/Tracer/FigTree), http://m […]

call_split

Genome wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

2018
Sci Rep
PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0
call_split See protocol

[…] constructed using the maximum likelihood method using JTT + G as a best model. SBP domain amino acid sequences were converted to the PHYLIP format and analysed with the PhyML3.0 software (http://www.atgc-montpellier.fr/phyml/), which uses the approximate likelihood-ratio test (aLRT) and depends on a non-parametric Shimodaira-Hasegawa-like (SH-like) approach. […]

call_split

Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae

2018
PLoS One
PMCID: 5931646
PMID: 29718949
DOI: 10.1371/journal.pone.0196466
call_split See protocol

[…] analyses based on nucleotide data, the most appropriate model GTR + G was selected by jMODELTEST using the Akaike Information Criterion (AIC). The ML analysis was conducted with PhyML 3.0 (http://www.atgc-montpellier.fr/phyml/) and 1000 bootstraps were used to assess the support of nodes. BI was performed using MrBayes 3.1.2 []. In the case of the Bayesian analysis, the Markov Chain Monte Carlo we […]

call_split

Recognition of the genus Thaumatophyllum Schott − formerly Philodendron subg. Meconostigma (Araceae) − based on molecular and morphological evidence

2018
PMCID: 5943393
PMID: 29750071
DOI: 10.3897/phytokeys.98.25044
call_split See protocol

[…] 000 generations with four chains, which were sampled every 100th cycle. We have applied a burn-in of 20%. Individual gene trees were used to estimate a supertree with PhySIC_IST algorithm (http://www.atgc-montpellier.fr/physic_ist/) in order to avoid the impact of missing data in the estimation ().We have also performed phylogenetic analysis for concatenated chloroplast markers separated from nucl […]

call_split

First cases of European bat lyssavirus type 1 in Iberian serotine bats: Implications for the molecular epidemiology of bat rabies in Europe

2018
PLoS Negl Trop Dis
PMCID: 5933805
PMID: 29684025
DOI: 10.1371/journal.pntd.0006290
call_split See protocol

[…] Maximum Likelihood (ML) and Maximum Parsimony (MP). ME was obtained through a Neighbor-Joining algorithm with MEGA7 (http://www.megasoftware.net/), ML was constructed with PHYML software (http://www.atgc-montpellier.fr/phyml/) and finally, MP trees were inferred with PAUP* 4.0b10 (http://paup.csit.fsu.edu/) weighting transversions differentially according to the transitions/transversion ratio of […]

library_books

Persistence of the ABCC6 genes and the emergence of the bony skeleton in vertebrates

2018
Sci Rep
PMCID: 5902450
PMID: 29662086
DOI: 10.1038/s41598-018-24370-7

[…] final edited alignment was used as the input for the construction of phylogenetic tree by: Bayesian inference (BI) in MrBayes and Maximum Likelihood (ML) implemented in PhyML 3.0 software (http://www.atgc-montpellier.fr/phyml/), using the SMS automatic model selection, for protein evolutionary analysis according to the AIC (Akaike Information Criterion).BI analysis was performed using an LG substi […]

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ATGC institution(s)
Lawrence Berkeley National Laboratory, Berkeley, CA, USA

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