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Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences, based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here we analyze a model of codon evolution under an idealized genetic code and demonstrate that those p...
Different frequencies amongst codons that encode the same amino acid (i.e. synonymous codons) have been observed in multiple species. Studies focused on uncovering the forces that drive such codon usage bias showed that a combined effect of mutational biases and translational selection works to produce different frequencies of synonymous codons. Ho...
A substitution represents the emergence and fixation of an allele in a population or species and is the fundamental event from which phylogenetic models of sequence evolution are devised. As a result of the increasing availability of genomic sequences, we can currently leverage interspecific variability while reconstructing the tree of life. Substi...
I've been using Primer3 software (SantaLucia and Breslauer algorithm) and the Beacon software, and as I've been getting very different results among the different softwares and algorithms. I was wondering if any one knows which one is the most trustworthy.
I worked at a laboratory and before extracting DNA, I washed of the ethanol with Tris-HCl, in order to get rid of all the ethanol before starting the extraction process, but I did not understand why it needs to be completely washed off. Can anyone explain to me why is this such an important step?