Jukes-Cantor correction - Revision history

Christoph at 23:40, 20 June 2008

2008-06-20T23:40:49Z

Christoph at 05:30, 25 May 2008

2008-05-25T05:30:19Z

Christoph at 04:52, 13 September 2006

2006-09-13T04:52:07Z

Christoph: /* References */ fixed reference

2005-12-30T23:55:38Z

‎References: fixed reference

Christoph: Started article

2005-12-30T23:49:30Z

Started article

New page

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 makes these counts not a desirable measure of distance. In some way, this slow down must be accounted for.

The solution to this problem was first noted by Jukes and Cantor (1969). Instead of calculating distance as a simple count take the distance as

<pre>K(A,B) = -3/4 * loge[1 - 4/3 * D(A,B)]</pre>

This is the '''Jukes-Cantor correction equation''' for [[homoplasy]].

== Example ==

* Un-corrected distance:

<pre>
* * * *
Species A: ATGCT CGTAG CTGCT ACGTC
Species B: ATCCT CGAAG CAGCT ACGAC
</pre>

Count the changes (*) and divide by the length:

<pre>D(A,B) = 4/20</pre>

* Jukes-Cantor correction distance:

<pre>
A B
Species A: ---- 0.20
Species B: 0.23 ----
</pre>

Apply the equation above to these data.

== References ==
* Kimura and Ohta (1972). ''J Mol Evol'' '''2''':87-90.
* Jukes TH and Cantor CR (1969). Mammalian Protein Metabolism ("Evolution of protein molecules"). ''Academic Press'' (New York; H. N. Munro edition).

[[Category:Academic Research]]
[[Category:Phylogenetics]]

@@ Line 35: / Line 35: @@
 * Jukes TH and Cantor CR (1969). ''Mammalian Protein Metabolism'', H. N. Munro, Ed. (Academic Press, New York), pp. 21-132.
-[[Category:Academic Research]]
+{{Phylogenetics}}
 [[Category:Phylogenetics]]

@@ Line 6: / Line 6: @@
 This is the '''Jukes-Cantor correction equation''' for [[homoplasy]].
-== Example ==
+==Example==
-−
 * Un-corrected distance:
@@ Line 30: / Line 29: @@
 Apply the equation above to these data.
-== References ==
+==References==
 * Kimura and Ohta (1972). ''J Mol Evol'' '''2''':87-90.
 * Jukes TH and Cantor CR (1969). ''Mammalian Protein Metabolism'', H. N. Munro, Ed. (Academic Press, New York), pp. 21-132.
 {{Phylogenetics}}
 [[Category:Phylogenetics]]

@@ Line 1: / Line 1: @@
 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 makes these counts not a desirable measure of distance. In some way, this slow down must be accounted for.
-The solution to this problem was first noted by Jukes and Cantor (1969). Instead of calculating distance as a simple count take the distance as
+The solution to this problem was first noted by Jukes and Cantor (1969). Instead of calculating distance as a simple count take the distance as:
+<center>[[Image:Jukes-Cantor correction equation.png]]</center>
-<pre>K(A,B) = -3/4 * loge[1 - 4/3 * D(A,B)]</pre>
 This is the '''Jukes-Cantor correction equation''' for [[homoplasy]].