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Knowledge of Curriculum - includes knowledge of the content goals to be addressed at particular grade levels, as well as the K-12 vertical alignment of evolution goals and ways in which evolution connects to other topics in the horizontal curriculum.
Based upon Magnusson et al. (1999) model of PCK, teachers should develop knowledge for teaching evolution in the following categories: Knowledge of Curriculum - includes knowledge of the content goals to be addressed at particular grade levels, as well as the K-12 vertical alignment of evolution goals and ways in which evolution connects to other topics in the horizontal curriculum.
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The likelihood is calculated as the probability of obtaining the data (multiple sequence alignment) given the model of evolution (substitution model and phylogeny).
Within the Mollusca, where the sequence composition is highly variable between clades, both alignment methods and models of evolution used in phylogenetic analyses at date still remain the main bottlenecks in tracing deep phylogeny.
The composition of each column in these alignments is the result of evolution and it will usually differ markedly from a neutral distribution.
Besides the comparative matrix view, users may explore the multiple sequence alignment and evolution of either mature or precursor miRNA sequences from miRBase, our prediction results, and user-supplied sequences via incorporated CLUSTALW [ 40] and Jalview [ 41].
Not all sites in an alignment have the same rate of evolution.
On the basis of the multiple sequence alignment, we estimated the rate of evolution for each CP sequence in order to infer the selective constraints.
For each gene family, a region excluding known protein-coding sequence was selected for alignment, thus nearly neutral rates of evolution can be assumed.
These concatenation-derived trees were compared with the individual gene trees by first pruning the concatenation-derived tree to the same taxa as the gene tree using DendroPy (Sukumaran and Holder 2010) and then retrieving the per-site log likelihoods of both trees using RAxML based upon the gene alignment and the same model of evolution (WAG + Γ + F).
Finally, we analyzed both nucleotide and amino-acid alignments under time-heterogeneous models of evolution.
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