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In addition we tested adaptive evolution using the maximum-likelihood based approach implemented in the program PAML v3.15 (Yang 1997).
To estimate divergence times we followed a Bayesian based approach implemented in the software Multidivtime [ 29, 34].
To investigate the substructure in the transcriptomes of late larvae and adult worms, we ordered all transcriptomes using a PCA based approach implemented in the software BLIND [ 29].
For the quantitative assessment of the number of groups in the panel, a Bayesian clustering analysis was performed using a model based approach implemented in the software package STRUCTUREv 2.2 [ 46, 47].
Estimate of the time to the most common ancestor (TMRCA) was obtained using a phylogeny based approach implemented in NETWORK 4.5 using a mutation rate based on the number of fixed differences between chimpanzee and humans.
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For 4,297 (51.0%) of the annotated CDS, a function could be automatically inferred using a number of sequence similarity based approaches implemented in the GenDB auto-annotator METANOR [ 16].
For this purpose, as well as for the linear absorption spectrum calculations, we adopted an INDO model Hamiltonian [21] based approach implemented recently in a computer program developed by us [22].
To corroborate this claim, in (Segall et al. 2011) a BDD-based approach, implemented in the Focus tool, was better in terms of cost than the greedy solutions Advanced Combinatorial Testing System (ACTS) (Yu et al. 2013), Pairwise Indepedent Combinatorial Testing (PICT) (Czerwonka 2006), and jenny (Jenkins 2016) in the constrained domain.
A linear regression model of the log-transformed VEGF on age was applied and the residuals were used as a quantitative trait in the multipoint quantitative linkage analysis on each sub-pedigree set using the regression-based approach implemented in MERLIN-REGRESS [27].
The model-based approach implemented in STRUCTURE 2.1 was used at the Bioportal server [ 76].
The model-based approach implemented in software package STRUCTURE [ 17] was used to examine population structure.
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