Software Available for Download

• SSA: Inference of Maximum Likelihood Phylogenetic Trees Using a Stochastic Search Algorithm
  
  This program implements the stochastic search algorithm for estimation of phylogenetic trees under the maximum likelihood criterion. It is described in the following paper for trees which satisfy the molecular clock, although it can estimate non-clocklike trees as well:
  
  Salter, L. and D. Pearl. 2001. A Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees, Systematic Biology 50(1): 7-17.
  
  Click here to download the program.
  
  
  
• SSAMK: Inference of Maximum Likelihood Phylogenetic Trees for Morphological Data
  
  This program uses a stochastic search algorithm for estimation of maximum likelihood phylogenetic trees for morphological data, using the model of Lewis (Syst Biol 50(6): 913-925). The search algorithm is similar to that described in the Salter and Pearl paper above.
  
  Please contact me if you'd like to use this program.
  
  
  
• Phylogenetic Utility Programs
  
  This includes programs to aid in the summary of the posterior distribution of phylogenetic trees from the program MrBayes. The first program, post_prob, will tabulate the percentage of times each tree topology appears in the posterior distribution output by MrBayes, thus providing posterior probabilities for each tree topology. The second program, post_root, will tabulate the percentage of times each possible root position appears in the posterior distribution output by MrBayes, thus providing posterior probabities for each root.
  
  Click here to download these programs.
  
  
  
• NEW!!!STEM: Species Tree Estimation using Maximum likelihood
  
  STEM is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model.
  
  Click here to download the program.
  
  
  
• COMING SOON!!STEM-hy: Species Tree Estimation using Maximum likelihood with HYbridization
  
  If you would like to be notified when this program is released, please e-mail me: lkubatko --at-- stat.osu.edu.
  
  
  
• COAL: Program for computing gene tree probabilities under the coalescent process
  
  Written by James Degnan (Ph.D., Spring 2005) - please see the COAL Website for more information and to download the program.
  
  
  
• FPRNET: Program for detecting gene regulatory networks from gene expression data using fuzzy logic, probability, and regression methods.
  
  Written by Guy Brock (Ph.D., Summer 2003) - please see the FPRNET website for more information and to download the program.
  
  
  
• Analysis of High-throughput Proteomic Data
  
  Programs to perform the analysis in the following reference are available:
  
  Gilchrist, M., L. Salter, and A. Wagner. 2004. A statistical framework for interpreting high-throughput proteomic datasets, Bioinformatics 20(5): 689-700.
  
  Click here to download these programs.