User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/03/04

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Big Picture Comparative Phylogenetics

  • A Task View on Phylogenetic Comparative Methods (in R on CRAN) has been released today, maintained by Brian O'Meara. Quite thorough and concise.
  • Follow-up discussion on:
    • List is useful, but would be nice to be able to expand / collapse the list to see more / less details about the functions available. More detail makes it harder to maintain, perhaps get the developers involved?
    • List is also quite provocative source to realize what's missing (there's no way to estimate ancestral states under OU using existing software?) I'm interested in exploring a way users could both suggest and then rank / vote for certain requests to be implemented, in the style of uservoice or stackoverflow. Piloting an example of this during the phylogenetics workshop at Bodega.

1:30 pm Meeting with Tom Near, visiting from Yale. Chance to discuss both projects in this notebook:

  • Inferring multistate optima and transitions.
  • Assessing power in trees; bootstrapping model fits.

2pm 4pm Installing software for Bodega Phylogenetics Workshop next week. Some packages are Linux friendly, others less so. Java packages are particularly useful/reliable as cross-platform apps.

  • BEAST -- Java
  • BEST -- C compiles fine with make.
  • Brownie -- C++ won't compile (no configure script)
  • FigTree - Java
  • Garli -- C++, requires Nexus Class Library installed (C++ library which installs fine with configure, make, make install). However Garli still refuses to compile with enough errors to make me feel a header file is missing (things undefined, stdio.h undeclared, etc).
  • Mesquite -- Java
  • Phylocom -- R, src (in C, which compiles fine with make), directory also contains Win and Mac binaries
  • MrBayes -- Is in the Ubuntu repositories, just apt-get it. Rock on!
  • RaxML -- C, just run the gcc version of the makefile. Haven't tried the MPI version
  • Tracer -- Java

4pm EVE Seminar: Tom Near

  • Antarctic fishes as an example of an adaptive radiation. Fossil record shows cosmopolitian mix of species: skates, labrids, sharks, cods. At the time the continent was farther north and warmer (geological record and δO18 isotope describes temperature.) Mass extinction, followed by invasion of this antarctic group with protein for antifreeze that rapidly radiates into dominant fish diversity form in the region. Strong result for much faster speciation relative to nearby groups.