Sentence examples for using the ml package from inspiring English sources

The optimisation procedure was coded in Stata 8 and Stata 9 (StataCorp, 2003, 2006), using the ML package.

The codeml program from the PAML package (Yang 2007) was used to calculate dN and dS using the ML method (using the options seqtype = 1, runmode = -2 and CodonFreq = 2 in the codeml.ctl files).

Selection was assessed using the ML method in the Codeml program of the Phylogenetic Analysis by Maximum Likelihood (PAML) 4.7 package (Yang 2007).

All ML trees were constructed using the Phylip package [ 27].

ML phylogenetic analyses were conducted using the Phyml package (Guindon and Gascuel 2003), with 1,000 bootstrap replicates, and the GTR+I+G substitution model.

Based on the new alignment, phylogenetic trees were constructed using three different methods: NJ with ClustalW software [ 85], MP using the PAUP package [ 86] (p-distance) and ML using the TREE-PUZZLE package with the default parameters [ 87].

ML classification (Scheres et al, 2007) was performed using the XMIPP package (see Supplementary Materials and methods).

We next reconstructed ML ancestral states at each site for all ancestral nodes using the software package Lazarus (Hanson-Smith et al., 2010).

The statistical analysis were performed using the R statistical package and the effsize package (Torchiano 2017).

Data were analyzed using the R package.

Statistical analysis was performed using the Statistical Package for the Social Sciences 13.0 software package.