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For this purpose, sequences that had been classified as false positives in the synthetic dataset and uniquely classified in the experimental metagenome dataset were analysed using MEGABLAST.
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The population structure of the 3K-RG dataset was analysed using ADMIXTURE software46 on the core SNP set (version 0.4, http://snp-seek.irri.org/download.zul).org/download.zul
The same dataset was analysed using Mx (Neale 2004).
Here, the full dataset was analysed using GeneSpring GX 10.0.2 (previously, we used GeneSpring GX 7.3.1).
The combined dataset was analysed using partition specific model parameters [ 73].
The dataset was analysed using Stata version 11.0 (StataCorp Inc., College Station, TX, USA).
The concatenated dataset was analysed using mixed models for 77 single gene partitions.
ITS dataset was analysed using maximum likelihood and Bayesian approaches as described above (see multi-gene phylogenetic analyses section).
The same dataset was analysed using the software Mx (Neal 2004) for ML-estimation in twin- and family studies.
The final dataset was analysed using the MIXED procedure of SAS with a model that included breed, diet and their respective interaction as independent variables.
The same dataset was analysed using a SOM-based clustering method, AutoSOME, which placed all samples into 7 major clusters, with Sso_1D and Sso_33C highlighted as singletons.
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