Computational protocol: Control of yeast retrotransposons mediated through nucleoporin evolution

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Protocol publication

[…] Gene sequences from six species of Saccharomyces yeasts were obtained from publically available online resources. Maximum likelihood analysis of dN/dS was performed using the codeml program in PAML 4.1. Multiple protein sequence alignments were created and were manually curated to remove ambiguities before processing with PAL2NAL to produce accurate DNA alignments []. DNA alignments were fit to two models: M7 (codons fit to a beta distribution of dN/dS values, with dN/dS > 1 disallowed) and M8 (similar to model 7, but with dN/dS > 1 allowed). One model of codon frequency (f61) and a seed value of 0.4 for dN/dS (ω) was used (). Likelihood ratio tests were performed to evaluate which model of evolution the data fit significantly better with positive selection and inferred if we can reject M7 in favor of M8 with a p<0.05. REL and FEL codon based models were also used to detect sites under positive selection as implemented by the HyPhy package using the best substitution models chosen by Akaike information criterion (AIC) using the phylogenetic tree (Newick format):((((S. paradoxus, S. cerevisiae), S. mikatae), S. kudriavzevii), S. arboricolus, S. bayanus) (). […]

Pipeline specifications

Software tools PAML, PAL2NAL, HyPhy
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Saccharomyces cerevisiae, Toxoplasma gondii, unidentified retrovirus, Viruses