Computational protocol: Association between GNRHR, LHR and IGF1 polymorphisms and timing of puberty in male Angus cattle

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Protocol publication

[…] Allele frequencies, unbiased expected heterozygosity (he) and Hardy-Weinberg equilibrium (HWE) for each SNP within each herd and for the whole sample were estimated using exact test implemented in GENEPOP 4 [] and ARLEQUIN 3.5 [] softwares. Phases were reconstructed with the Bayesian statistical method implemented in Phase v2.1.1 [,] using default options, except that the program was run five times and the last iteration was 10 times longer, as suggested by the authors. Phases were considered reliable when P value estimated by Phase was higher than 0.8. […]

Pipeline specifications

Software tools Genepop, Arlequin
Application Population genetic analysis
Organisms Bos taurus