ModelTest-NG

[…] onstruction and estimation of the divergence times among the five long-tailed pheasants were achieved using BEAST with the GTR+G model, which was selected as the best nucleotide substitution model by Modeltest and PAUP*. We added two nodes as the fossil calibration points according to the TimeTree database, including Elliot's pheasant-Reeves's pheasant (11.1 Mya) and Elliot's pheasant-Mrs. Hume's […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]