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Statistical analysis was run with SPSS 14 software.
Item 12 'flourescein' was removed and a forced three PAF analysis was run with the remaining 14 items.
The Bayesian analysis was run with MrBayes 3.1.2 [68].
The analysis was run with 100000 MCMC steps and five chains.
The post hoc analysis was run with the use of the Tukey test.
The analysis was run with 2×105 generations, and the first 5×104 were discarded as burn-in.
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These two forms of transcript analysis were run with independent samples (plants grown independently).
FunWalk analysis was run together with NetWalk, and a FunTable corresponding to scores of functional terms associated with subnetworks of increased or decreased gene expression was generated.
The analysis was run twice, with 20 million generations per run (total 40 million generations).
The analysis was run twice with 2 × 106 generations each, and the first 10% of parameter values were discarded as burn-in.
Each analysis was run twice with 4 chains (one cold, three heated), 5 million MCMC generations and a sample frequency of 100.
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