Sunday, March 28, 2010

Looking to open access (preferably w/ CC licenses) review papers covering introduction to phylogenetic trees and methods

I am teaching a class this spring and as part of the class am having one lecture on "Phylogenetic trees and methods." I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good?


  1. Hmm, blogger ate my comment, so a bit more brief this time.

    1) This 2008 paper by St├ęphane Aris-Brosou and Xuhua Xia reviews the statistical methods used in the entire phylogenetics life-cycle

    2) This paper by Sean Carroll reviews the efforts and reasons for failure in hard-to-resolve phylogenies

    3) This paper by Hanno Sandvik discusses the problems that students can have when thinking about trees, and include some practice questions.

    All these papers are released under some form of CC Attribution License.

  2. Oh, my comment lives! Sorry about the double-posting.

  3. Not sure about the licensing issues, but I like this one:

    "Phylogeny for the Faint of Heart." Great title. It is 2003, so might be out of date.

  4. A technicla paper for the basic and optimized Sankoff's parsimony under cost matrices:

    Clemente et al. 2009. Optimized ancestral state reconstruction using Sankoff parsimony. Bioinformatics 10: 51.

  5. Great - thanks all - some of these are excellent

  6. Some suggestions from twitter:

    @phylogenomics How about this one:

    @pathogenomenick: @phylogenomics these slides from nick matzke caught my eye recently


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