Software
The software listed below is some of what will be used at the workshop.For all the R packages listed please make sure to install all dependencies too (i.e. all the other packages that the package requires to work). **Please download all of the software in this list before you arrive at the workshop.**
Phylogeny Estimation
![[WWW]](http://wikispot.org/wiki/eggheadbeta/img/sycamore-www.png){kind=small}
MrBayes 3.2.1 RAxML v7.2.8 (Scroll down for download)
Divergence-Time Estimation
BEAST v1.7.0
starttree: A Unix program for generating a starting tree
Model Selection
MCMC Diagnosis
Tracer v1.5 TreeSetViz v0.906 AWTY (online server) iMCMC (For Mac Users, scroll down for download) MCRobot (For PC Users, scroll down for download))
Character Evolution
Discrete Traits
BayesTraits v1.0 Mesquite v2.7.4 PDAP (this is an add on module for Mesquite) SIMMAP v1.5
Continuous Traits (including phenotypic diversification)
R-package: ape R-package: phytools R-package: OUCH v2.7.1 R-package: geiger v1.3.1 R-package: auteur R-package: qpcR R-package: pmc R-package: nlme R-package: reshape
Diversification Rates
SymmeTREE v1.0 R-package: Diversitree v0.6.3 R-package: laser v2.3 R-package: APE v2.6.3 R-package: TreeSim v1.0
General purpose
FigTree R (and several packages, follow the link to a tutorial on what to do) TextWrangler (Mac only) EditPad lite (PC only) ActivePerl (PC only, most of you will want the 'Windows (x86) MSI') snowfall v1.84 (for parallel computing)
