Simon Whelan

发表

Automated Removal of Non-homologous Sequence Stretches with PREQUAL.

Iker Irisarri, Fabien Burki, Simon Whelan, 2020, Methods in molecular biology.

Pandit: a database of protein and associated nucleotide domains with inferred trees

Simon Whelan, Nick Goldman, Paul I. W. de Bakker, 2003, Bioinform..

Determination and validation of principal gene products

Alfonso Valencia, Jennifer L. Harrow, Michael L. Tress, 2008, Bioinform..

A graph-based approach for improving the homologyinference in multiple sequence alignments

Simon Whelan, Raja Hashim Ali, Marcin Bogusz, 2018 .

PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences

Iker Irisarri, Fabien Burki, Simon Whelan, 2018, Bioinform..

GeLL: a generalized likelihood library for phylogenetic models

Simon Whelan, Daniel Money, S. Whelan, 2015, Bioinform..

Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome

Carolin Kosiol, Simon Whelan, Lee Bofkin, 2006, J. Biomed. Informatics.

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

Nicolas Rodriguez, Simon Whelan, Nick Goldman, 2005, Nucleic Acids Res..

Determining the evolutionary history of gene families

Simon Whelan, Simon C. Lovell, Daniel Money, 2012, Bioinform..

Measuring the distance between multiple sequence alignments

Simon Whelan, Benjamin P. Blackburne, S. Whelan, 2012, Bioinform..

A novel use of equilibrium frequencies in models of sequence evolution.

Simon Whelan, Nick Goldman, S. Whelan, 2002, Molecular biology and evolution.

Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable.

Simon Whelan, Christian Peter Klingenberg, C. Klingenberg, 2020, Systematic biology.

Class of multiple sequence alignment algorithm affects genomic analysis.

Simon Whelan, Benjamin P. Blackburne, S. Whelan, 2013, Molecular biology and evolution.

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.

David Haussler, Francesca Chiaromonte, Mark Diekhans, 2003, Genome research.

The prevalence of multifurcations in tree-space and their implications for tree-search.

Simon Whelan, S. Whelan, Daniel Money, 2010, Molecular biology and evolution.

Physicochemical amino acid properties better describe substitution rates in large populations

Simon Whelan, Claudia C Weber, S. Whelan, 2018, bioRxiv.

Statistical Methods in Molecular Evolution

Simon Whelan, S. Whelan, R. Nielsen, 2005 .

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.

James E. Allen, Simon Whelan, David Talavera, 2015, Systematic biology.

Characterizing the phylogenetic tree-search problem.

Simon Whelan, S. Whelan, Daniel Money, 2012, Systematic biology.

Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics

Simon Whelan, Nick Goldman, S. Whelan, 1999 .

New approaches to phylogenetic tree search and their application to large numbers of protein alignments.

Simon Whelan, S. Whelan, 2007, Systematic biology.

Covariation Is a Poor Measure of Molecular Coevolution

Simon Whelan, David Talavera, Simon C. Lovell, 2015, Molecular biology and evolution.

Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes

Simon Whelan, Nick Goldman, S. Whelan, 2004, Genetics.

Spatial and temporal heterogeneity in nucleotide sequence evolution.

Simon Whelan, S. Whelan, 2008, Molecular biology and evolution.

Phylogenetic substitution models for detecting heterotachy during plastid evolution.

Simon Whelan, Benjamin P. Blackburne, Matthew Spencer, 2011, Molecular biology and evolution.