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The last sentence of the 2nd paragraph needs to be referenced: Even though it is sub-optimal in this sense, it has been extensively tested and usually finds a tree that is quite close to the optimal tree.
Who tested it?
In the algorithm description:
"Find the pair of taxa in Q with the lowest value. Create a node on the tree that joins these two taxa (i.e. join the closest neighbors, as the algorithm name implies)." -- It is not clear to me how the joining of two taxa works. while the method is probably specific to the given data, at least the general criteria for the joined object should be mentioned.
91.89.65.97 (
talk) 09:13, 29 July 2008 (UTC)
Time and space complexity of this algorithm? -- TobiasBengtsson ( talk) 20:47, 17 November 2008 (UTC)
The statement "In the example above, this formula would give a distance of 6 between A and the new node and a distance of 1 between B and the new node." appears to be wrong. For the distance between A and the new node, I get 7/2 + 17/4. Tedtoal ( talk) 01:20, 27 August 2010 (UTC)
I think there is another problem with the example. When i compute the value Q(A,B) with the given formula for the Q-matrix, i get -26 and not -40 as stated in the examples Q-matrix. The same is true for the other values in the Q-matrix. It appears that to compute the values in the example the first term of the formula for Q(i,j), namely (r-2)d(i,j), is omitted. As i am just a layman in this field, i don't know which is correct (i guess it is the formula) but either the formula or the computed example is wrong.-- 85.91.175.222 ( talk) 08:38, 4 October 2011 (UTC)
Is it correct to say NJ is for construction of "phenetic trees"? Phenetics seems to be grouping based on similarity, rather on (inferred) evolutionary relationships. I suggest saying "phylogenetic trees" rather than phenetic. Objections? — Preceding unsigned comment added by Tomfy ( talk • contribs) 16:03, 16 February 2012 (UTC) Saitou and Nei's original NJ paper's title is "The Neighbor-joining method: A New Method for Reconstructing Phylogenetic Trees." So I think it is fair to replace 'phenetic' with 'phylogenetic' here (which I have done). tom fisher-york ( talk) 16:53, 6 April 2014 (UTC)
Is the time complexity of the algorithm really O(n^3)? It takes n-3 iterations to complete a tree with n taxa, and there are n^2 elements in the Q matrix. But for each element in the Q matrix, one has to cycle through all elements k=1...n such that k is not equal to i or j. This adds another factor of n-1. So wouldn't the complexity by O(n^4)? Calculating the matrix takes n^3 steps, and this has to be done n times, roughly speaking. 71.166.127.224 ( talk) 21:25, 21 March 2014 (UTC)
The figure at the right seems false, and quite unsettling to me.
JPLeRouzic ( talk) 10:58, 11 December 2016 (UTC)
Agreed regarding the racist implications of the figure. From the perspective of Saitou Naruya, this is a quite-possibly-innocent example of what scientists call "hypercontextualization", a term for when facts and figures alone have a misleading conclusion when divorced from their broader context. The Neighbor-joining method inherently creates an unrooted tree, and the figure conforms unremarkably to the usual default way that scientists represent an unrooted tree: by putting the genetic center of gravity in the center of the figure. The tree can't help but recapitulate the literal geography of human migrations, and since the trans-caucasian region between Europe, Arabia, the Pontic Steppe, and India is geographically in between East Asia, Malesia, Oceania, and the Americas, the human genes here are indeed shown to represent that. However, other scientific facts tell us that the genetic root of the tree is not located at the geographic center of gravity of the populations represented in that figure, and as encyclopedists, we must never let minor details give a misleading impression of a broader picture; thus, that figure is too hypercontextualized to be appropriate for this general encyclopedic context. I'm thus going to remove it, with a note in the edit log that anyone reverting or re-adding the figure ought to name their reasons for doing so here. Signed, TheMigratoryPlatypus 67.3.121.25 ( talk) 22:02, 28 February 2018 (UTC)
This article is rated C-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | ||||||||||||||||||||||||||||||||||
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The last sentence of the 2nd paragraph needs to be referenced: Even though it is sub-optimal in this sense, it has been extensively tested and usually finds a tree that is quite close to the optimal tree.
Who tested it?
In the algorithm description:
"Find the pair of taxa in Q with the lowest value. Create a node on the tree that joins these two taxa (i.e. join the closest neighbors, as the algorithm name implies)." -- It is not clear to me how the joining of two taxa works. while the method is probably specific to the given data, at least the general criteria for the joined object should be mentioned.
91.89.65.97 (
talk) 09:13, 29 July 2008 (UTC)
Time and space complexity of this algorithm? -- TobiasBengtsson ( talk) 20:47, 17 November 2008 (UTC)
The statement "In the example above, this formula would give a distance of 6 between A and the new node and a distance of 1 between B and the new node." appears to be wrong. For the distance between A and the new node, I get 7/2 + 17/4. Tedtoal ( talk) 01:20, 27 August 2010 (UTC)
I think there is another problem with the example. When i compute the value Q(A,B) with the given formula for the Q-matrix, i get -26 and not -40 as stated in the examples Q-matrix. The same is true for the other values in the Q-matrix. It appears that to compute the values in the example the first term of the formula for Q(i,j), namely (r-2)d(i,j), is omitted. As i am just a layman in this field, i don't know which is correct (i guess it is the formula) but either the formula or the computed example is wrong.-- 85.91.175.222 ( talk) 08:38, 4 October 2011 (UTC)
Is it correct to say NJ is for construction of "phenetic trees"? Phenetics seems to be grouping based on similarity, rather on (inferred) evolutionary relationships. I suggest saying "phylogenetic trees" rather than phenetic. Objections? — Preceding unsigned comment added by Tomfy ( talk • contribs) 16:03, 16 February 2012 (UTC) Saitou and Nei's original NJ paper's title is "The Neighbor-joining method: A New Method for Reconstructing Phylogenetic Trees." So I think it is fair to replace 'phenetic' with 'phylogenetic' here (which I have done). tom fisher-york ( talk) 16:53, 6 April 2014 (UTC)
Is the time complexity of the algorithm really O(n^3)? It takes n-3 iterations to complete a tree with n taxa, and there are n^2 elements in the Q matrix. But for each element in the Q matrix, one has to cycle through all elements k=1...n such that k is not equal to i or j. This adds another factor of n-1. So wouldn't the complexity by O(n^4)? Calculating the matrix takes n^3 steps, and this has to be done n times, roughly speaking. 71.166.127.224 ( talk) 21:25, 21 March 2014 (UTC)
The figure at the right seems false, and quite unsettling to me.
JPLeRouzic ( talk) 10:58, 11 December 2016 (UTC)
Agreed regarding the racist implications of the figure. From the perspective of Saitou Naruya, this is a quite-possibly-innocent example of what scientists call "hypercontextualization", a term for when facts and figures alone have a misleading conclusion when divorced from their broader context. The Neighbor-joining method inherently creates an unrooted tree, and the figure conforms unremarkably to the usual default way that scientists represent an unrooted tree: by putting the genetic center of gravity in the center of the figure. The tree can't help but recapitulate the literal geography of human migrations, and since the trans-caucasian region between Europe, Arabia, the Pontic Steppe, and India is geographically in between East Asia, Malesia, Oceania, and the Americas, the human genes here are indeed shown to represent that. However, other scientific facts tell us that the genetic root of the tree is not located at the geographic center of gravity of the populations represented in that figure, and as encyclopedists, we must never let minor details give a misleading impression of a broader picture; thus, that figure is too hypercontextualized to be appropriate for this general encyclopedic context. I'm thus going to remove it, with a note in the edit log that anyone reverting or re-adding the figure ought to name their reasons for doing so here. Signed, TheMigratoryPlatypus 67.3.121.25 ( talk) 22:02, 28 February 2018 (UTC)