Edward Susko

Department of Mathematics and Statistics
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

Munoz-Gomez, S., Susko, E., Williamson, K., Eme, L., Slamovitz, C.H., Moreira, D. Purificacion, L. and Roger, A.J. (2021). A site-and-branch-heterogeneous model on an expanded dataset favor mitochondria as sister to known Alphaproteobacteria. Nature Ecology & Evolution. 6:253--262. link

Baker, B.A, Gutierrez-Preciado, A., Rodiriguez del Rio, A., McCarthy, C.G.P., Lopez-Garcia, P., Huerta-Cepas, J., Susko, E., Roger, A.J., Eme, L. and Moreira, D. (2024). Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nature Microbiology. 9:964--975. link

Williamson, K., Eme, L., Banos, H., McCarthy, C., Susko, E., Kamikawa, R., Orr, R.J.S. Munoz Gomez, S., Minh, B.Q., Simpson, A.G.B. and Roger, A.J. (2024). A robustly rooted tree of eukaryotes reveals their excavate ancestry. link
software documentation and source code Software and documentation last updated November 22, 2024.

Jones, C.T., Youssef, N., Susko, E. and Bielawski, J.P. (2020). A Phenotype-genotype Codon Model for Detecting Adaptive Evolution. Systematic Biology. 69:722--738. pdf
software and documentation This software is provided by Chris Jones, who should be contacted if you have any questions. Software and documentation last updated January 12, 2021.

Susko, E., Lincker, L. and Roger, A.J. (2018). Accelerated Estimation of Frequency Classes in Site-heterogeneous Profile Mixture Models. Molecular Biology and Evolution. 9:1266--1283. pdf
software documentation and source code Source code last updated: Apr 7, 2022. Documentation last updated: Apr 7, 2022.

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.

Wu, J. and Susko, E. (2009). General heterotachy and distance method adjustments. Molecular Biology and Evolution. 26:2689--2697. html or pdf
software documentation and source code Software last updated: June 20, 2018.

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: November 1, 2021.

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.