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

Susko, E., Lincker, L. and Roger, A.J. (2018). Accelerated Estimation of Frequency Classes in Site-heterogeneous Profile Mixture Models.

software documentation and source code Source code last updated: September 11, 2018. Documentation last updated: September 11, 2018.

Wang, H., Susko, E. and Roger, A.J. (2016). Split-specific Bootstrap Measures for Quantifying Phylogenetic Stability and the Influence of Taxon Selection.

software documentation and source code Software last updated: October 27, 2016.

Susko, E. (2015). Bayesian Long Branch Attraction Bias and Corrections

software documentation and source code Software last updated: November 28, 2014.

Susko, E. (2014). Tests for Two Trees using Likelihood Methods.

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.

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.

software documentation and source code Software last updated: September 5, 2012.

Susko, E. (2011). Improved Least Squares Topology Testing and Estimation.

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.

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.

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.

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.

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.

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.

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.

software documentation and source code Software last updated: March 10, 2018.

Susko, E. (2003). Confidence Regions and Hypothesis Tests for Topologies Using Generalized Least Squares.

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.

software documentation and source code

Susko, E. (2003). Weighted Tests of Homogeneity for Testing the Number of Components in a Mixture.

software documentation and R source code file Software last updated: Aug 3, 2017.