User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/03/08
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Bodega Phylogenetics Workshop Day 2Marine lab researchers are back, and network speeds have just about given up (down to bytes/s). This post is composed offline and will be uploaded to the notebook. Details are well logged on the Bodgea Phylogenetics Wiki so these are reasonably sketchy with my comments. My Updates to Bodega Phylogenetics WikiMade several contributions to the Bodega Phylogenetics Wiki today:
Today's agenda
Brian Moore: BEAST8:30 - 9:30a Diving into the XML and actually running BEAST. Wiki page. Bob Thompson: Species Tree vs Gene Tree9:45
Differences are common and Widespread! Pollard et. al. (2006), PMID:17132051 BEST: Bayesian Estimation of Species Trees Works with MrBayes, build on MrBayes Greg Pauly, RAxMLReally large trees can be done no other way. (Garli works, but doesn't permit partitions or amino acid based inference). Rich Glor, Introduction to R1:30 p
Brian Moore, Model Selection and MCMC diagnosisslides Estimation under the prior alone! Brian's scripts for keeping track of what parameters he's tried. Very interesting idea. (We didn't actually get through all 181 slides...)
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