Software Tanja Stadler

The package TreeSim provides quick methods to simulate phylogenetic trees, the package TreePar allows for diversification rate estimation on given phylogenies, and Beast provides tools for phylogenetic tree reconstruction.

• R package TreePar 2.2 available on CRAN. Implemented by Tanja Stadler. Latest Version: November 1st, 2011.
  R package for inferring speciation and extinction rates based on phylogenetic trees.
  CITATION:
  Stadler, T, Mammalian phylogeny reveals recent diversification rate shifts, Proc. Nat. Acad. Sci. (2011) 108:6187-6192.
• R package TreeSim 1.5 available on CRAN. Implemented by Tanja Stadler. Latest Version: November 1st, 2011.
  R package for simulating phylogenetic trees.
  CITATION:
  Stadler, T, Simulating trees on a fixed number of extant species, Syst. Biol. (2011);
  Hartmann, K, Wong, D, Stadler, T, Sampling Trees from Evolutionary Models Syst. Biol. (2010) 59:465-476;
  Stadler, T, On incomplete sampling under birth-death models and connections to the sampling-based coalescent, Syst. Biol. (2009) 261:58-66
• Beast Bayesian Evolutionary Analysis Sampling Trees by Alexei Drummond and Andrew Rambaut.
  The birth-death prior is implemented using the results from: Stadler, T, The conditioned reconstructed process, Jour. Theo. Biol. (2008) 253:769-778.
  The birth-death prior with incomplete sampling is implemented using the results from: Stadler, T, On incomplete sampling under birth-death models and connections to the sampling-based coalescent, J. Theo. Biol. (2009) 261:58-66.
  The birth-death prior with sampling through time is implemented using the results from: Stadler, T, Sampling-through-time in birth-death trees, J. Theo. Biol. (2010) 267:396-404.
• Cass Implemented by Tanja Stadler. Last update - May 18th, 2009.
  A Python tool for analyzing and manipulating phylogenetic trees (simulating trees under birth-death processes with incomplete sampling, estimating dates in supertrees, testing for neutrality with our runs statistic, the Colless statistic, drawing LTT plots etc). Details are found in the ReadMe.
  Installing Python on your computer is easy and straightforward, so it should not prevent you from using the Cass package! An installation guide is included in the ReadMe of the Cass package.
  CITATION:
  Stadler, T, Lineages-through-time plots of neutral models for speciation, Math. Biosc. (2008) 216:163-171.
• TreeSample Implemented by Klaas Hartmann.
  Program for simulating phylogenetic trees with a fixed number of species.
  CITATION:
  Hartmann, K, Wong, D, Stadler, T, Sampling Trees from Evolutionary Models, Syst. Biol. (2010) 59:465-476.