Sentence examples for used the codeml program from inspiring English sources

We used the codeml program implemented in PAML package for the selection test.

For each coding sequence, we used the codeml program of the PAML 3.15 [24] suite to conduct a likelihood ratio test between different evolutionary models.

We used the codeml program in the PAML v.3.14 [18] package to estimate the non-synonymous divergence (dN), synonymous divergence (dS), and their ratio (dN/dS) in model 0, that allows for a single dN/dS value throughout the whole phylogenetic tree.

For all analyses of positive selection we used the codeml program from the PAML package [ 16].

We used the codeml program in the PAML package [ 26] version 3.14 to perform likelihood ratio tests of positive selection.

We used the CODEML program within the PAML suite (Yang 2007) to calculate the ML-based d N/d S (denoted as ωML) for the pairwise comparison of Mb sequences obtained from the simulations.

We conducted analyses of positive selection using the codeml program in the PAML 4.3 package [66].

Two likelihood ratio tests of positive selection were implemented using the codeml program [13], [37], [38].

Test of positive selection on single codons was performed using the codeml program in the package PAML 3.15 [49].

Tests for selection and ancestor sequence reconstruction were carried out using the Codeml program implemented in PAML [35], [36].

The data in each sliding window were analyzed using the codeml program in the paml package [13] to fit codon model M0 (one ratio).