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The study characteristics of 83 datasets were coded.
In stages (4) and (5) data from disciplinary datasets were coded across and between the 12 units.
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Afterwards the composed datasets are coded as XRFF files.
Alleles in the dataset were coded using A and B and pairwise IBS was computed between all samples.
4) Using the code book, the qualitative dataset was coded in Nvivo 8 [ 64], a qualitative data analysis program.
However, less than five trials in both datasets combined were coded as 'inadequately concealed', making lack of retention of these three categories less likely to result in bias in this study.
The phylogenetic analyses were performed on a constrained topology and the combined dataset (the missing data were coded by "?") using maximum likelihood (ML) as implemented in PAUP* v.4b.0.
In the genetic dataset, homozygous marker genotypes were coded as -1 and 1, and the heterozygous type, missing values and technical failures were coded as 0. 58.7%% of the markers corresponded to homozygous alleles and 16.1 % were heterozygous.
An additional 530 gaps and indels in the combined dataset of all DNA regions were coded using the algorithm described by [ 28] in the FastGap v1.2 interface [ 29].
Datasets taken from the different studies were coded accordingly.
Subsequently, gaps were coded for each dataset using the Simple Gap Coding method of Simmons and Ochoterena [ 71 ], as implemented in SeqState v.1.4.1 [ 72 ].
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