An improved Fisher information-based optimization procedure was also designed to ascertain the optimal mask parameters corresponding to specific bandwidth.
Within this step CLASlite 3.0 offers the a standard set of masking parameters, which use optical and thermal channels from Landsat to remove conservatively mask or remove portions of the image that contain atmospheric phenomena like haze, clouds, cloud edges and shadows, and topographic shade [17].
We employed both immediate recall and forced choice category recognition tasks to assess the efficacy of the backward masking parameters in our study.
As masking effectiveness depends not only on the duration of the targets, but can also depend on other variables (qualitative characteristics of both the targets and the masks, stimulus onset asynchrony, etc)., we also conducted explicit assessments (described next) to determine the effectiveness of our backward-masking parameters.
To circumvent this issue, we sought to establish the best repeat masking parameters for the grapevine genome.
To determine the appropriate masking parameters to use in this study, we conducted a factorial experiment in which 36 parameter combinations were tested (see Methods).
Our findings, which mostly rely on intact scrambled comparisons across SF and exposure duration, thus cannot be due to divergent masking parameters.
Within this step CLASlite 3.0 offers the a standard set of masking parameters, which use optical and thermal channels from Landsat to remove conservatively mask or remove portions of the image that contain atmospheric phenomena like haze, clouds, cloud edges and shadows, and topographic shade [ 17].
To determine the optimal alignment masking parameters, the following REAP parameter values were tested: window sizes of w = 3, 6, sum-of-pairs threshold scores of s c = 0.5, 1.0, 1.5, column gap thresholds of g c = 0.1, 0.2, 0.5, and sequence gap thresholds of g s = 0.5, 0.7.
For other Asclepiadoideae, we made reduced random read pools providing approximately 125× sequencing depth of the plastome, or used all reads if <125× depth was obtained, and then conducted reference-guided assembly in Alignreads using the A. nivea sequence as a reference, the medium similarity setting, and the masking parameters and evaluation criteria of Straub et al. (2012).
Repeat sequences were identified by Repeat Masker version 3.3.0 with Repbase version 15.08, and the following parameters: -no_is, -norna, -engine, -s, -parallel = 1; and Repeat Protein Mask with parameters: -noLowSimple, -pvalue = 1e-4 [ 65].
