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The probabilities of identity by sexual reproduction were calculated using the software package GENCLONE 2.0 [48], which implements a method that takes into account the FIS estimated from each population [49] as S. hystrix is known to show some level of self-fertilisation [32] and deviations from HWE were observed in some of the sampled populations.
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We have implemented a method that addresses these issues by incorporating phylogenetic analyses, multilevel regression with mixed effects, and false discovery rate (FDR) control.
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We designed and implemented a method that fits an inverse power law model to points of a given learning curve created using a small annotated training set.
I recently implemented a method that allows for computing RELL (Resampling Estimated Log Likelihoods) bootstrap support as described by Minh et al. (2013).
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A key motivation for implementing a method that can predict RNA RNA interactions between two multiple alignments of RNA sequences is the existence of many ncRNA candidates identified by genome-wide in silico screens as mentioned before.
When estimating the rate of substitution at CpG sites, it is clearly preferable to implement a method that explicitly models context-dependent evolution, such those proposed in refs [ 3, 4, 22] or [ 23].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com