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Ideally, the best sequence data come from direct dating of many points.
Thus, it is of major importance to obtain the best sequence data possible and to create the most accurate multiple sequence alignments.
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The simplest model of sequence evolution that best fits the sequence data (GTR+G) was determined under the Akaike Information Criterion (AIC) in jModeltest 0.1.1 [40], [40].
To determine the simplest model of sequence evolution that best fits the sequence data, the Hierarchical Likelihood Ratio Test (hLRT) and Akaike Information Criterion AICC) were implemented using MrModeltest 1.1b [62], [62] in each data set.
MODELTEST 3.7 [ 68] was run for each partition to choose the model of molecular evolution that best fit our sequence data.
To best fit the sequence data for the hexon gene, we used the DNA/Protein model test to identify the optimal evolutionary model, GTR+Γ+I (general time reversible + gamma + invariable).
The likelihood ratio test implemented in ModelTest 3.06 [ 62] found the TrN + I + G model best fitting the sequence data, and this model was employed in a heuristic ML analysis.
Additionally, for the additional file 2, a ML analysis of mutagenized populations of FMDV was performed by means of the program Modelgenerator [ 61], useful to identify the optimal evolutionary model (Akaike Information Criteria and Hierarchical Likelihood Ratio Test indicated that the GTR model best fit the sequence data).
Prottest [ 45] was used to chose the best model for protein sequence data and the AIC criteria to determine the scheme of data partitioning.
We selected the GTR+ Γ +I model since it was found by the MEGA5 software [ 46] to provide the best fit to the sequence data.
We used MODELTEST version 3.06 [ 45] to determine the minimum parameter nucleotide substitution model that best fit the mtDNA sequence data under the Akaike Information Criterion [ 46].
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