Talk:Neighbor joining

message: 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?
:Yeah, that's a really bad statement. The basic idea is that neighbor-joining assumes rates-across-sites. So if you generate your data under a rates-across-sites model, then you can be fairly sure that you'll get pretty good results. So neighbor-joining is only "suboptimal" in the sense that it requires the rates-across-sites assumption to do well. I'll look for a reference for this. --Wzhao553 20:10, 21 February 2006 (UTC)
replies: text: Actually, there is a precise answer. A distance matrix is called additive if it can be specified by a tree with distances along the edges. NJ works if the given distance matrix d is 'close' to additive. The precise notion is given in one of the references of the article (why NJ works). --Jochgem (talk) 15:38, 18 April 2008 (UTC)

text: I'm currently trying to improve the article, and I added what a naive implementation would result in. Probably the faster methods out there give more details in their papers, but I haven't looked at them yet 134.58.42.46 (talk) 08:58, 16 March 2011 (UTC)

text: My implementation gets the "right" values (6 and 1), maybe I should finish the example originally posted by "???" 134.58.42.46 (talk) 08:58, 16 March 2011 (UTC)

text: In the sums in the formula for Q(i,j) the index k runs over all values including i and j, so for Q(A,B), the sums are (7 + 11 + 14) = 32, and (7 + 6 + 9) = 22. These get subtracted from 2 d(A,B) = 14;  Q(A,B) = 14 - (32 + 22) = -40.  — Preceding unsigned comment added by 24.59.127.24 (talk) 04:30, 9 February 2012 (UTC)
replies: text: That is different from what it says in the description of the Q matrix.  It says "k is any other node not i or j".  Based on the description, I got Q(1,2) = -26 as well.  So the description is either un-clear or the example does not follow it.  Captkrob (talk) 21:01, 3 January 2014 (UTC)
replies: text: Ditto this. This is still a problem, but it is unclear what the solution should be. A reference text, such as Biological Sequence Analysis (Durbin, et al.) gives a slightly different formula altogether.  — Preceding unsigned comment added by 131.111.184.92 (talk) 16:56, 25 January 2014 (UTC)
replies: text: The solution is to remove "k is any other node not i or j respectively"; k should take on all values from 1 to r. I think the "respectively" was meant to mean that k=i is excluded from the first sum, an k=j is excluded from the second sum, which would make it right, but since d(i,i) = 0, it doesn't matter whether we exclude these or not, so it's simpler just to let the sum run over all k=1 to r. I have fixed it. tom fisher-york (talk) 17:43, 26 March 2014 (UTC)

text: I believe the answer is that the sums from k=1 to r which appear in the formula for Q(i,j) do not have to be evaluated from scratch with each iteration. When two leaves are joined, two terms are lost from each of these sums, and are replaced by a new term (the distance to the newly created node).tom fisher-york (talk) 17:07, 26 March 2014 (UTC)
thread_title: Comments

message: The figure at the right seems false, and quite unsettling to me. 
* It presents the "Caucasoid" in a central place, and "Negroid" at a larger distance of "Caucasoid" than other groups. I think that we now know that the "homo sapiens" has its origin in Africa. Genome analysis shown that European, Asian groups are derived from the African homo sapiens, with possibly incorporation of genes from other human species such as Neanderthal. So "Caucasoid" (whatever it means) should not be in the center of the figure.
* We know also that Bantu are genetically closer to European that they are close to San or Khoi (the correct name for the people that inhabited Sub-Saharan Africa before Bantu migration).
* I have some problem to understand the distinction between Nigerian and Bantu as Bantu is a human group with its origins in Southern Nigeria and Cameroon.
* And finally, even if English is not my native tongue, I do know that words like "negroid", "Bushmen" are derogatory.
JPLeRouzic (talk) 10:58, 11 December 2016 (UTC)
thread_title:  Weird, possibly racist figure