Sentence examples for used methods implemented in from inspiring English sources
We used methods implemented in DATAMONKEY [ 31] and CODEML to investigate whether positive selection has also driven the evolution of the avian IFITM gene family.
A total of 1000 runs were performed per Aegilops subset, and results from runs minimizing the intragroup variance were reported (we used methods implemented in the 'e1071' R CRAN package).
We inferred the population demographic history using methods implemented in the package ∂a∂i (version 1.60), which is based on the joint site frequency spectra between multiple populations16.
Affymetrix microarray data were analyzed using methods implemented in the R/Bioconductor platform.
Sex specific life expectancy at birth with 95%% confidence intervals was calculated using methods implemented in an online Microsoft Excel spreadsheet that is provided by the Max Planck Institute for Demographic Research.
Raw counts were normalized and variance-stabilized values were obtained using methods implemented in the DESeq package [ 26] in R. Present and absent calls were generated by fitting the normalized values to a two-component Gaussian distribution function using the EM algorithm implemented in the mixtools package in R [ 20].
Thyroid function parameters were determined using methods implemented at the Department of Nuclear Medicine in Innsbruck.
We used regression methods implemented in SPSS software (SPSS 14.0, Chicago, IL, USA) to impute missing values.
We used regression methods implemented in SPSS software (SPSS 14.0, Chicago, IL, USA) to impute missing values (<3% for the scored imaging characteristics).
First we used two methods implemented in DATAMONKEY [ 60] for detecting positive selection: the "Mixed Effects Model of Evolution" (MEME) and the "Fast Unbiased Bayesian Approximation" (FUBAR).
Maximum likelihood trees (as described above) of each of the five Macaronesian clades were used to estimate divergence dates using Bayesian methods implemented in Multidivtime [57], [58].
