Edward Susko

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

----------------------------------------------------------------------

Telephone: (902) 494-8865
Fax : (902) 494-5130
Office: Room 202 in the Chase Building
email: edward.susko@gmail.com
mail: Department of Mathematics and Statistics
         Dalhousie University
         Halifax, Nova Scotia
         Canada B3H 4R2

Software


- Wang, H., Susko, E. and Roger, A.J. (2016). Split-specific Bootstrap Measures for Quantifying Phylogenetic Stability and the Influence of Taxon Selection. Molecular Phylogenetics and Evolution.105:114--125. pdf
software documentation and source code Software last updated: October 27, 2016.

- Susko, E. (2015). Bayesian Long Branch Attraction Bias and Corrections Systematic Biology.64:243--255. pdf
software documentation and source code Software last updated: November 28, 2014.

- Susko, E. (2014). Tests for Two Trees using Likelihood Methods. Molecular Biology and Evolution. 31:1029--1039. pdf
software documentation and source code Software last updated: January 9, 2014.

- Zou, L., Susko, E., Field, C. and Roger, A.J. (2012). Fitting Nonstationary General-time-reversible Models to Obtain Edge-lengths and Frequencies for the Barry-Hartigan Model. Systematic Biology. 61:927--940. pdf
software documentation and source code as well as the required lapack library source code (version 3.3.1) if it is not available on your system. This software is provided by Liwen Zou , who should be contacted if you have any questions. Software last updated: April 26, 2012.

- Susko, E. and Roger, A.J. (2012). The Probability of Correctly Resolving a Split as an Experimental Design Criterion in Phylogenetics. Systematic Biology. 61:811--821. pdf
software documentation and source code Software last updated: September 5, 2012.

- 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: September 4, 2012.

- 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: March 17, 2015.

- 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 Software last updated: Aug 3, 2017.

----------------------------------------------------------------------