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A script that performs the READemption and TSSAR based analysis can be retrieved from https://zenodo.org/record/17358 (DOI: 10.5281/zenodo.17358).
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A full development of the rank-based analysis can be found in Chapters 3-5 of the monograph by [Hettmansperger and McKean (2011]).
A comparison of the Flory–Huggins and decoy-based analysis can be found in the Supplementary Materials.
Our current analysis is focused on general behaviors across Poeciliids, more species-based analysis can be found in Bierbach et al. (2013) (in press).
They also show that a model-based analysis can be used to validate the accuracy of field plots by calculating predictions with a model based on different subsets of the plots.
Our study also indicates that haplotype-based analysis can be much more powerful than marker-by-marker analysis.
Screening descriptors calculated through a semi-empirical model, we demonstrate how an informatics-based analysis can be used to address this issue with no prior assumptions.
In principle, this level of design-based analysis can be applied to any protein, paving the way toward identifying and understanding the hallmarks of the thermodynamic and structural limits of function.
There are numerous other scenarios where gel-based analysis can be useful.
The computation of the rank-based analysis can be obtained by using the R package RfitRfit.
The computation of a rank-based analysis can be obtained by using the R package Rfit Rfit developed by [Kloke and McKean (2012]), which can be downloaded at CRAN.
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Justyna Jupowicz-Kozak
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