What is Jukes Cantor correction?
The Jukes-Cantor correction solves the problem in phylogenetics when as the time of divergence between two sequences increases the probability of a second substitution at any one nucleotide site increases and the increase in the count of differences is slowed. This is the Jukes-Cantor correction equation for homoplasy.
Why is the P distance considered as an underestimated value?
The p-distance is an underestimation of the true genetic distance because some of the nucleotide positions may have experienced multiple substitution events.
What are P distances?
This distance is the proportion (p) of nucleotide sites at which two sequences being compared are different. It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared.
What is the 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 general time reversible 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 the difference between P distance and D distance?
As in the case for nucleotide sequences, the p-distance is merely the proportion of different amino acids between two sequences compared. Therefore, the statistical properties of this distance are the same as those of the p-distance for nucleotide sequence data….p-distance.
| p = nd/n, | (4.48) |
|---|---|
| V(p) = p(1 – p)/n | (4.49) |
What is a Upgma tree?
UPGMA (unweighted pair group method with arithmetic mean; Sokal and Michener 1958) is a straightforward approach to constructing a phylogenetic tree from a distance matrix. It is the only method of phylogenetic reconstruction dealt with in this chapter in which the resulting trees are rooted.
How does the Jukes-Cantor distance model work?
Jukes-Cantor distance. In the Jukes and Cantor (1969) model, the rate of nucleotide substitution is the same for all pairs of the four nucleotides A, T, C, and G. As is shown below, the multiple hit correction equation for this model produces a maximum likelihood estimate of the number of nucleotide substitutions between two sequences.
When to use Jukes-Cantor distance for nucleotide substitution?
However, when the number of nucleotides examined is small, say n< 100, the Jukes-Cantor distance tends to give overestimates of the true number of nucleotide substitutions (Tajima 1993). Table 4.1 Models of nucleotide substitution
How did Charles Cantor calculate the genetic distance?
To overcome this problem Charles Cantor and Thomas Jukes developed a probabilistic model and derived the following formula to calculate genetic distances: where K is the genetic distance and d is the number of observed substitutions divided by the sequence length. They also found the variance of K could be found by: