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The assessment calculations were performed using the default calculation model options implemented in the code.
The number of generated poses was set to 20, without the early termination option, and the default calculation mode was selected.
The default calculation parameters were adjusted to cope with the large number of markers.
Similar(57)
(The above default FST calculation represents the case with n = 1).
Sequence conservation analysis of APC and activators genes was conducted using the BLAST tool with default curve calculation parameters; amino acids sequence "conservation similarity" of 50%.
Sequence conservation and microsynteny analysis of Populus gene models with Populus homeologous (duplicated) genomic regions and the Arabidopsis genome was conducted using the Vista Browser tool with default curve calculation parameters; nucleotide sequence 'conservation identity' of 70% and 'minimum conservation width' of 100 bp [ 52].
Average nucleotide identity (ANI) was calculated using whole-genome sequence data for the 35 Vibrio strains using the JSpecies program version 1.2.1 (Richter and Rosselló-Móra 2009) with default settings for calculation of ANIb.
For IFP similarity calculations, default settings were kept.
How extensive where the simulations/optimizations? What were the energy cutoffs?... All DFT and QM/MM calculations used Gaussian09 default convergence criteria for SCF calculation and geometry optimisation: a statement to this effect has been added to the methods section.
For BN kinship calculation, the default command was used: emmax-kin -v -h -d 10.
A value of True (default) means do the calculation, and False means redisplay the existing values.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com