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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).
The combined dataset was analysed using partition specific model parameters [ 73].
The concatenated dataset was analysed using mixed models for 77 single gene partitions.
Here, the full dataset was analysed using GeneSpring GX 10.0.2 (previously, we used GeneSpring GX 7.3.1).
The dataset was analysed using Stata version 11.0 (StataCorp Inc., College Station, TX, USA).
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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.
When the query dataset is analysed using all three different programs with the Species-excluded and Genera-excluded databases, it is shown that lower sensitivity scores are obtained in higher order taxonomic levels, namely in the order and family levels.
Each of the simulated datasets was analysed using the four approaches described above.
All reconstructed datasets were analysed using VivoQuant software (v2.0, inviCRO, LLC, Boston, USA).
Where appropriate, differences between datasets were analysed using a two-tailed paired Students T test.
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