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We performed a phylogenetic analysis on the total evidence data set (all four genes combined) using Maximum Likelihood (ML) method with RAxML [ 100] and a file to partition the alignment by codon position and gene.
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The MP analysis of the mitochondrial genes together resulted in one tree (see Supplementary Material, 'Mitochondrial results', Figure S4), and likewise the total-evidence data set ('Total-evidence results', Figure S5).
To convince the regulators completely, a number of "totality of evidence" data sets need to be provided to them for thorough evaluation.
In this study, data sets, checklists, and structured reporting protocols for pathologic examination and reporting of cutaneous melanoma were analyzed by an international panel of melanoma pathologists and clinicians with the aim of developing a common, internationally agreed upon, evidence-based data set.
Similar results were found when selectivity bias in the models were checked using the two different exclusion criteria [(i) 'number of children' via empirical evidence in the data set, and (ii) 'number of children', 'region of residence' and 'health status' via evidence from literature].
There was no evidence in the data set indicative of Hardy Weinberg disequilibrium (P=0.92).
There is further evidence in our data set for this observation by a significant overrepresentation of lysine acetylation-modified transcription factors in the same lymphoid tissues.
There was no evidence in the data set for population stratification based on testing the distribution of SNP genotypes for Hardy Weinberg disequilibrium.
However, under the principle of total evidence, the combined data set may result in novel relationships being revealed [ 31, 33] and therefore could contribute important information to the supertree.
There is evidence in our data set for a signature of population expansion in the rabai clade, with individuals sampled from inland localities (Morogoro District, Kidugallo, Kingolwira, Nguu) primarily having haplotypes shared or derived from coastal populations.
However, when markers from PMA25A and PMA25B were mapped together in a single linkage group, there was relatively weak evidence of linkage between markers on these linkage groups in the NL data set and no evidence in the UK data set.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com