Talk:Maximum parsimony (phylogenetics)
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Good article, anon, but I wish to improve it to clarify some points and possibly make it more accessible.
OLD: Maximum parsimony
Maximum parsimony is a simple but popular technique in bioinformatics to predict the best phylogenetic tree for an organism.
Maximum parsimony is a simple but popular technique used in cladistics to predict an accurate phylogenetic tree for a set of taxa (commonly a set of species or reproductively-isolated populations of a single species.
Comments: The level 2 heading 'maximum parsimony' is redundant - have replaced with 'Introduction'. 'Bioinformatics' has been replaced with 'cladistics' because the former is more of a broad approach to biological research than a specific field of research. Have removed 'best' from introduction as this does not scientifically-describe the criteria for an optimal tree - 'accurate' is better. In addition, 'best' could be inferred as stating that MP is the best method to produce a tree when there is no consensus that any method is the best under all circumstances. Have also replaced 'organism' with 'set of taxa' and given two examples of appropriate sets to compare.
--ChrisJMoor 00:59, 16 Feb 2005 (UTC)
There needs to be some mention of bootstrapping. Jim Bowery 18:57, 18 July 2005 (UTC)
I've done the best I can with what is here, but it would be great if, in the future, someone could break this out into separate artciles for different classes of data, types of analysis, and optimality criteria. As it is, the MP entry is pretty much holding down the entire subject of character-based phylogenetics, which isn't ideal. And, of course, citations would really help alot. Everything in the article is supported, honest. Google Hillis. 18.104.22.168 02:26, 1 January 2007 (UTC)
Cleanup taskforce: you are doing a really good job with this article!22.214.171.124 15:06, 10 July 2007 (UTC)
- Mmmm, also looks to me like there may be more than a little shtuff that needs to be moved to some other article(s), such as the paragraph beginning: "Neighbor-joining is a form of star decomposition..." Will do as time permits. --Ling.Nut 07:31, 26 August 2007 (UTC)
Great job editing this page!
- Agree on the "alternatives" material: I do hope some of it can be salvaged...
- The "criticism" is not Original Research... most of these criticism IS in fact published, but finding references is not going to be pleasant. Some of the RESPONSES may be even more difficult to find references for.
- I haven't read the "self-referencing" guidlines, but I never actually CITED myself. For what it is worth.
'Maximum' considered unnecessary
"Maximum parsimony" is not the correct title for this article - the word "maximum" is implicit in the term "parsimony" and its usage... So many seem to get this wrong!' Ryan —Preceding unsigned comment added by 126.96.36.199 (talk • contribs) 26 March 2008
clarify "Problems with maximum parsimony pylogeny estimation"
I have a hard time understanding the example in this section. In the first paragraph, it is referred to "charactes (A & C)", but surely these are taxa?
Then, is the figure supposed to represent the actual relationship, or the calculated (MP) tree?
While I see the point with only one character, won't the many substitutions (another word could profitably be used here, this seems to assume we're working on a molecular level) between branches A and D ensure that the tree will be more accurate when more characters are taken into account?
Several times throughout the article, it is said that it's not good to exclude input data only because they have gaps/wildcards. Probably a valid point, but there's no need to hammer. (I also wonder how biologists can use such ad-hoc elimination methods on their data in seemingly arbitrary fashion, without a mathematical proof that they are useful, but maybe I'm misinterpreting the text.)--188.8.131.52 (talk) 04:38, 12 January 2009 (UTC)
There's a citation needed tag about inconsistency of ML with suboptimal models. The citation is Farris, James S., 1999. Likelihood and Inconsistency. Cladistics 15, 199–204. — Preceding unsigned comment added by 184.108.40.206 (talk) 15:58, 3 August 2011 (UTC)
Minimum evolution redirects here, but I don't think it should. MP and ME are different approaches, and there is no mention of ME in this article. In the absence of a separate article on 'minimum evolution', how about having a min evolution section in 'computational phylogenetics', and redirecting there? Objections?tom fisher-york (talk) 01:55, 5 March 2012 (UTC)
A stab at a simplified lead
I didn't think the lead was serving the needs of an intelligent middle-schooler at all well, so I made rather aggressive structural changes to the lead, while denting the actual text as little as possible—though I did add my own explanatory text concerning the core challenge of phylogenetics to help set the stage. Having not massaged the original text, the revised structure is not as smooth as it might be (and there are some obvious warts). I encourage anyone with a sense of appropriate language in this subject domain to further polish the flow. — MaxEnt 10:51, 12 January 2015 (UTC)
technical content swizzle in lead
I took a second stab to make the lead more comprehensive and less essayish in tone, bumping the last two paras off the lead into a new section titled "Alternate characterization and rationale" (admittedly an ugly limbo) and replacing these two paragraphs with substantive concerns lifted from the main article and mildly restructured for reading level. — MaxEnt 11:23, 12 January 2015 (UTC)