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We list these different properties of a method in Supplementary Note 2, along with a brief discussion about their algorithmic approach, important parameters, and directions to freely available implementations.
See a Supplementary Method in Supplementary file 1 for details.
In fact, SA-IS uses an almost-identical 'induced-sorting' procedure to sort the substrings in the divide phase as well (section 'The Method' in supplementary material).
In an experiment where very large selective advantages are expected, more regular sampling would be beneficial for the purposes of this method (in Supplementary Tables, we have applied a heuristic cut off such that f i >0.5→0.5 in order to prevent these events biasing the reported fitness ratio statistics).
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A detailed description of the method is in Supplementary Methods.
Details are provided as the Supplementary Methods in Supplementary Information.
For each physiochemical property, the coevolution scores of SSEs in contact were compared to the correlations of shuffled distance vectors (null model) (See Methods in Supplementary for details).
(A) Comparison of coevolution signals of various properties for all types of SSE pairs in contact and random SSE associations (null model) (see Methods in Supplementary).
The relative abundance of each type of DNA/ethidium complex can be calculated using the binomial distribution (Supplemental Methods in Supplementary Materials S1).
See, also, the Materials and Methods in Supplementary Data S1.
Detailed computational methods are in supplementary Methods, available at Annals of Oncology online.
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