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Protocols

ModelTest-NG specifications

Information


Unique identifier OMICS_30327
Name ModelTest-NG
Alternative name MODELTEST
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Programming languages C++, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.1.3
Stability Stable
Maintained Yes

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Documentation


Additional information


https://github.com/ddarriba/modeltest/tree/master/manual

ModelTest-NG citations

 (1765)
library_books

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] rch with 500 bootstrap replicates; then, the divergence time was analyzed using BEAST (BEAST, RRID:SCR_010228), version 2.3.2, with the GTR+I+Γ model, which is the best substitution model selected by Modeltest (version 3.7) and PAUP* (version 4.0a150) []. Four nodes were chosen as the fossil calibration points from the TimeTree database [], including human-chicken (311.9 Mya), anole lizard-chicken […]

library_books

BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

2018
PLoS One
PMCID: 5919079
PMID: 29694383
DOI: 10.1371/journal.pone.0193525

[…] zed for the analysis. A total of 307 unique sequences (including study sequences) of group B RSV focusing on the BA9 lineage were used (). PAUP 4.0 was used for inferring the phylogenetic tree [] and Modeltest3.7 program to estimate the nucleotide substitution rate []. The best model, favoured by Bay’s factor was calculated by path sampling and stepping stone sampling method [, ]. Three clock mode […]

call_split

Trypanosomatid parasites in Austrian mosquitoes

2018
PLoS One
PMCID: 5908168
PMID: 29672618
DOI: 10.1371/journal.pone.0196052
call_split See protocol

[…] ved manually in BioEdit (Ibis Therapeutics, Carlsbad, US). The final dataset contained 46 taxa and 1,988 nucleotide positions. Analyses were done in MrBayes [] and PhyML [] with model optimization in ModelTest [], version 3.06. A general time-reversible substitution model with a mixed model for among-site rate variation (GTR + Γ + I) was chosen as the best fitting model of sequence evolution. Boot […]

call_split

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)

2018
BMC Genomics
PMCID: 5907366
PMID: 29669515
DOI: 10.1186/s12864-018-4650-9
call_split See protocol

[…] Phylogenetic analyses were initially conducted using standard BI and ML analyses with homogeneous models. The datasets were not partitioned, and Modeltest 3.7 [] was used to infer the best substitution models for nucleotide data. BI analyses were conducted using GPU MrBayes []. In BI, the GTR + I + G substitution model for nucleotide data was […]

library_books

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species

2018
Sci Rep
PMCID: 5897349
PMID: 29651122
DOI: 10.1038/s41598-018-24126-3

[…] TS-2 variants detected in our study using DECIPHER and constructed maximum-likelihood (ML) phylogenetic trees using R phangorn package. We selected K80 + G as the best substitution model according to ModelTest. We used bootstrapping analysis to assess the integrity of phylogenetic trees. We visualized distribution of ITS-2 variants in individual hosts in the phylogenetic context using ggtree. As l […]

library_books

Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean

2018
BMC Evol Biol
PMCID: 5896055
PMID: 29642852
DOI: 10.1186/s12862-018-1167-4

[…] tion of expansion events []. BSP plots were generated for the geographic groups retrieved by SAMOVA. Analyses were carried out in BEAST version 1.7.5 considering a GTR model (as already calculated by MODELTEST version 3.7) and a strict molecular clock (confirmed as the best model fitting the examined intraspecific data when compared with lognormal relaxed molecular clock using Bayes factors (BF) m […]


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