Edward Susko

Professor
Department of Mathematics and Statistics
Center for Comparative Genomics and Evolutionary Bioinformatics
Dalhousie University

Telephone: (902) 494-8865
Fax : (902) 494-5130
Office: Chase 115
email: susko@mathstat.dal.ca
mail: Department of Mathematics and Statistics
         Dalhousie University
         Halifax, Nova Scotia
         Canada B3H 3J5

Software

Susko, E. (2011). Improved Least Squares Topology Testing and Estimation. Systematic Biology. 60:668--675. html or pdf
software documentation and source code or windows binaries Software last updated: April 15, 2011.

Susko, E. (2010). First-Order correct bootstrap support adjustments for splits that allow hypothesis testing when using maximum likelihood estimation. Molecular Biology and Evolution. 27:1627--1629. html or pdf
software documentation and source code or windows binary Software last updated: August 16, 2011.

Susko, E. and Roger, A.J. (2007). On reduced amino acid alphabets for phylogenetic inference. Molecular Biology and Evolution. 24:2139--2150. html or pdf
software documentation and source code or windows binary Software last updated: December 20, 2010.

Susko, E. (2006). Using minimum bootstrap support for splits to construct confidence regions for trees. Evolutionary Bioinformatics Online 2:137--151. pdf
software documentation and source code.

Susko, E., Leigh, J., Doolittle, W.F. and Bapteste, E. (2006). Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the γ-proteobacteria. Molecular Biology and Evolution 23:1019--1030. pdf
software documentation and source code. Cluster size software documentation and source code

Susko, E. and Roger, A. (2004). Estimating and comparing rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys. Bioinformatics. 20:2279--2287. pdf and supplementary material
software documentation and source code and commented R code for parametric estimation.

The software makes assumptions about input formats. John Hebert has kindly provided a Perl wrapper with documentation that will deal with more common formats.

Susko, E., Field, C., Blouin, C. and Roger, A.J. (2003). Estimation of rates-across-sites distributions in phylogenetic substitution models. Systematic Biology. 52:594--603. pdf
software documentation and source code Software last updated: August 16, 2011.

Susko, E. (2003). Confidence Regions and Hypothesis Tests for Topologies Using Generalized Least Squares. Molecular Biology and Evolution. 20(6):862--868. html or pdf
The software for this paper has been substantially revised so that covariance matrix estimates are better conditioned and more model options are available. Please see the software for Susko (2011) "Improved Least Squares Topology Testing and Estimation." listed above.

Susko, E., Inagaki, Y., Field, C., Holder, M.E. and Roger, A.J. (2002). Testing for Differences in Rates-Across-Sites Distributions in Phylogenetic Subtrees. Molecular Biology and Evolution. 19(9):1514--1523. pdf
software documentation and source code

Susko, E. (2003). Weighted Tests of Homogeneity for Testing the Number of Components in a Mixture. Journal of Computational Statistics and Data Analysis: Special Issue on Mixtures, 41:367--378. pdf
software documentation and R source code file