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ATGC specifications


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

Publication for Alignable Tight Genomic Clusters

ATGC citations


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

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: (MEGA), (PhyML), (jModeltest), (RDP), (BEAST/Tracer/FigTree), http://m […]


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

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 (, which uses the approximate likelihood-ratio test (aLRT) and depends on a non-parametric Shimodaira-Hasegawa-like (SH-like) approach. […]


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

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 ( 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 […]


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

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 ( 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 […]


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

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 (, ML was constructed with PHYML software ( and finally, MP trees were inferred with PAUP* 4.0b10 ( weighting transversions differentially according to the transitions/transversion ratio of […]


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

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 (, 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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