What is Kimura 2 parameter model?
The Kimura 2-parameter (K2P) Model is a Markov model of base substitution. It assumes the root distribution vectors describe all bases occurring uniformly in the ancestral sequence. It allows different probabilities of transitions and transversions.
What are models of sequence evolution?
In biology, a substitution model, also called models of DNA sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules (e.g., DNA sequences) represented as sequence of symbols (A, C, G, and T in the case of DNA).
What is Kimura 2 parameter distance?
Kimura’s two parameter model (1980) corrects for multiple hits, taking into account transitional and transversional substitution rates, while assuming that the four nucleotide frequencies are the same and that rates of substitution do not vary among sites (see related Gamma distance).
What is GTR model?
The general time reversible (GTR) model, also known as the general reversible (REV) model is even more complex and assumes different rates of substitution for each pair of nucleotides, in addition to assuming different frequencies of occurrence of nucleotides.
What is Jukes and Cantor model in molecular evolution analysis?
The Jukes and Cantor model is a model which computes probability of substitution from one state (originally the model was for nucleotides, but this can easily be substituted by codons or amino acids) to another. From this model we can also derive a formula for computing the distance between 2 sequences.
What is P distance?
p-distance This distance is merely the proportion (p) of nucleotide sites at which the two sequences compared are different. This is obtained by dividing the number of nucleotide differences (nd) by the total number of nucleotides compared (n). Thus, p = nd/n.
What is the Jukes and Cantor 1969 model?
JC69, the Jukes and Cantor 1969 model, is the simplest substitution model. There are several assumptions. It assumes equal base frequencies and equal mutation rates. The only parameter of this model is therefore , the overall substitution rate. As previously mentioned, this variable becomes a constant when we normalize the mean-rate to 1.
What is the Jukes-Cantor model?
The simplest way to do this is the Jukes-Cantor (1969) model. Imagine a nucleotide can mutate with the same probability to any other nucleotide, so that the mutation rates in all directions are equal and symbolized by .
Why does the Jukes-Cantor distance correction have different numbers?
If you look up the Jukes-Cantor distance correction in other places you may see different numbers. This is because there are different ways to scale mutation when you write down the model. One approach is to divide all the mutation rates by three ( /3), so that the total rate of mutation away from a state is .
What is the Cantor model of DNA substitution?
Jukes Cantor Model of DNA substitution. This is a convenient distribution to use in many cases where the probability of an individual event is rare, events occur independently, and we are thinking about intervals of continuous time (or space). Classic examples are the number of people in a line at the bank per hour,…