Sentence examples for maximum likelihood suite from inspiring English sources

As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software.

The CODEML program in the PAML (Phylogenetic Analysis using Maximum Likelihood) suite of software (ver. 4.4) (3) was utilized for estimating evolutionary rates (by convention designated as ω = d N/d S) although any similar methodology (e.g. HyPhy) can be used (4).

A phylogenetic tree, generated with phyML [ 37] under the HKY substitution model [ 38], was used as the starting phylogeny for the codeML program of the Phylogenetic Analysis by Maximum Likelihood (PAML) suite [ 39].

Briefly, following univariate tests of normality, mixed analysis of variance (ANOVA) models were fitted to expression values using maximum likelihood estimation and the SAS software suite (SAS Institute).

A program suite based on maximum likelihood and prior knowledge (such as a reference volume) about the structure to be determined (Scheres, 2012) has taken the field by storm.

All diffraction data were processed using the HKL2000 suite, and the crystal structures were solved using maximum likelihood molecular replacement program Phaser in the PHENIX software suite.

The remainder of the structure (linker between ABD domain and spectrin-like domain 1 as well as the EF-hands 1-2) were built manually in coot (Emsley et al., 2010 ) The model was refined against native data extending to 3.5 Å by iterations of maximum likelihood and TLS refinement as implemented in the PHENIX suite (Adams et al., 2010 ) and manual building in coot.

The starting parameters of the chosen models were then "optimized" using a Maximum Likelihood (ML) method with the Brent Powell algorithm in the phylogenetics software suite P4 (v. 0.90) [ 134].

The core genome alignment and maximum likelihood phylogeny was determined using the parsnp programme implemented in Harvest suite of tools [ 49], resulting in a core genome of 733,991 bp.

Maximum likelihood clustering analysis of the blinded results from both labs demonstrates general clustering from the suite of samples from any given subject, again demonstrating the accuracy of the data obtained at each institution.

The maximum likelihood estimation of synonymous (Ks) and non-synonymous (Ka) substitution rate was estimated using the yn00 module of the PAML4 suite [ 83].