Sentence examples for based method implemented in from inspiring English sources
The maximum likelihood based method implemented in the codeml program of the PAML package (v3.15) [ 38] was used to detect positive selection as well as identifying positively selected sites, when the number of related sequences was sufficiently high.
Therefore, we used a more powerful maximum-likelihood based method, implemented in the CodeML subroutine of the software PAML [ 63] which allows the rates of ω = dN /dS to vary among codons [ 31, 64].
Ancestral distributions were estimated on the Bayesian consensus phylogram under Maximum Parsimony using MacClade v4.0 [ 66] and under a dispersal-vicariance event based method implemented in DIVA 1.1 [ 83].
Confirmed evidence for linkage at the 6p22.3 locus was followed up with allelic association studies using the family based methods implemented in TRANSMIT [ 11].
In the present study, three methods were used: a distance-based method called ParaFit implemented in CopyCat [ 80] and topology (or tree -based metree -basedmethodsimplementednd TreeMap 3 (developed by Mine Charleston and available at http://sites.google.com/site/cophylogeny).
The ADMM-based method implemented in a practical system is proposed in Section 4. Section 5 demonstrates the performance of our scheme through numerical simulation, followed by the conclusion in Section 6.
In this work, the optimal aerodynamic design is achieved by applying a non-intrusive, gradient-free, CFD-based method implemented in the in-house software FORMA (Fluid-dynamic Opti-mizeR for turboMachinery Aerofoils), specifically developed for the shape optimization of turbomachinery profiles.
In the present study we use the resampling-based method implemented in the Bioconductor package "clusterStab" to determine both the optimal number of clusters and the statistical significance of the final clustering [18].
(i) The likelihood-based method implemented in the program GARD ([31]; http://www.datamonkey.org/GARD) was used to identify putative recombination and gene conversion breakpoints, employing a nucleotide substitution model specified by the HyPhy software package ([55]; http://www.hyphy.org).org
Ka and Ks were estimated in two ways: i) by using the PBL method [47], [48] implemented in DAMBE [46], [49], and ii) by the likelihood-based method implemented in the YN00 program in the PAML package with the resulting Ka and Ks designated by dN and dS, respectively in table 1 [50].
