Available Software
- 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.
Coming soon!
- 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.
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