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The minimal folding free energy (MFE) of the sequence was set to less than or equal to −30 kcal/mol.
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The sequence is set in the Harmons' basement and includes images of postmortem young children, unborn (or aborted) babies in jars, skulls, a Christening dress, a nurse's uniform, and a figure holding a pair of bloody hedge clippers.
The sequence is set to be noncoding with the option "-a N r".
Once the sequence is set, only simple back-and-forth movements are necessary for detection with no disturbance in droplet order being observed.
The threshold for grouping of the sequences was set at the second branching point of the dendrogram from the root.
The sequences are set to linear.
All other options in the program pertaining to the sequences were set to default during simulation.
We used an infinite-sites model, with S fixed as the number of segregating sites found, and the length of the simulated sequence was set to the length of the sequence analyzed (4,007 bp).
The variable to specify the maximum length of the spacer sequence was set as 100bp in the MISA setup file.
For the third scenario, the root sequence was set to a GC content of 0.9 and the θ parameter to 0.9 in all branches.
The score to extend a gap along the genome sequence was set at −2 and the score to extend a gap along the read sequence was set at −1.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com