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Of interest for many downstream analyses were predicted sites, DNA fragments between proximal restriction sites.
With increasingly complex genetic risk interaction models, results from many downstream analyses are at stake when misassigned alleles snowball.
Many downstream analyses in population genomics, such as selection tests or demographic inferences rely on the allele-frequency spectra [ 41].
This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation.
Given the importance of the concept of orthology in many genomic studies, reliable identification of orthologous genes is crucial for many downstream analyses.
However, it is possible that a lower cutoff may be sufficient for many downstream analyses, as suggested by a comparison between RRBS and Illumina Infinium 450 K array [ 13].
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And yet multiple sequence alignments (MSAs) are a fundamental prerequisite for many downstream comparative analyses, including phylogenetic inference.
Our results suggest that simpler algorithms, like cRBH and cRSD, might be better choices for many downstream evolutionary analyses than more complex ones in cases where the objective is to identify orthogroups and that the trend of several studies toward using more complex ortholog prediction strategies is not always justified.
Genome annotation is used to identify and denote function of different segments in a genome sequence [ 1] and forms a basis for many downstream genome analyses.
This is because the editing procedure removed many genes encoding ribosomal proteins from the downstream analyses because of their low standard deviation.
Despite the fact that read trees consistently contain some topological and branch-length errors, we hypothesized that downstream analyses that aggregate information across many branches of a tree might be robust to these errors.
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