Comparative biology is a dynamic young field, with new types of analyses and
associated software applications are appearing constantly. Although this makes for
exciting times, it can also make comparative biology a difficult field to learn and
master. Making matters worse, most of the available software is relatively user
unfriendly and characterized by a variety of alternative user interfaces and
idiosyncratic input formats. Over the years, several groups have attempted to bring all of the various phylogenetic comparative analyses into a programming environment.
Hi,
There is a package for R called Phylo. Ypu can get more information from http://bioinformatics.oxfordjournals.org/content/26/15/1907.full
I also recommend the papers attached. ¿What kind of data are you planning to use in your analysis?
Carlos Morantes
There are a bunch of ways, depending on what you suspect the relationships between the taxa will be. I like the review by Graham and Graham, C.H., and P.V.A. Fine. “Phylogenetic Beta Diversity: Linking Ecological and Evolutionary Processes Across Space in Time.” Ecology Letters 11, no. 12 (2008): 1265–1277.
You can also check out our paper on the topic if you are interested phylogenetic signal along environmental gradients:
Root, Heather T, and Peter R Nelson. “Does Phylogenetic Distance Aid in Detecting Environmental Gradients Related to Species Composition?” Journal of Vegetation Science 22, no. 6 (December 1, 2011): 1143–1148. doi:10.1111/j.1654-1103.2011.01320.x.
Our paper is a basically a response to the method described by Nipperess, David A., Daniel P. Faith, and Kyle Barton. “Resemblance in Phylogenetic Diversity Among Ecological Assemblages.” Journal of Vegetation Science (May 2010): no–no. doi:10.1111/j.1654-1103.2010.01192.x.
Their package is available in R. I am personally skeptical on how informative these techniques are for ecological analyses but I shall not digress ...
Hi everyone, I am in the same dilemma, however, I have found many troubles using the phylomatic software, I can not obtain a reading tree for R with the last version of this programm? Someone knows if it some problems with the last APG III tree??
Hi, Galo Buitron-Jurado , I know how to obtain a reading tree (i.e. taxa in newick format) for R by Phylocom software of phylomatic package. It works with the last APG III tree. Let me know what types of data are you like to analyze? I am using tree data with their abundance.
Dear , Peter Nelson. I am able to download all the articles other than “Resemblance in Phylogenetic Diversity Among Ecological Assemblages.” Journal of Vegetation Science (May 2010): no–no. doi:10.1111/j.1654-1103.2010.01192.x. Can you please give this article which I think be helpful for me?
Hey, Carlos Morantes-Ariza, a great thanks to you. Actually I am searching for such ecological papers which you have mentioned.
@ Peter Nelson:
A great thanks to Researcher Peter Nelson for giving me such an article.
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