Statistical Tests of Gamma-Distributed Rate Heterogeneity in Models of Sequence Evolution in Phylogenetics
Nick Goldman , and Simon Whelan
Molecular Biology and Evolution 17 ( 6) 975 -978
105
2000
Mining the phylogenetic signal for inferring the origin of mitochondria
Ding He , Simon Whelan , Sandra Baldauf
2014
A graph-based approach for improving the homologyinference in multiple sequence alignments
Raja Hashim Ali , Marcin Bogusz , Simon Whelan
2018
Examining sequence alignments using a model-based approach
Raja Hashim Ali , Marcin Bogusz , Simon Whelan
2018
Selection acting on indels and substitutions in protein coding sequences
Marcin Bogusz , Simon Whelan
2018
New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments
Simon Whelan
Systematic Biology 56 ( 5) 727 -740
34
2007
The interface of protein structure, protein biophysics, and molecular evolution.
David A. Liberles , Sarah A. Teichmann , Ivet Bahar , Ugo Bastolla
Protein Science 21 ( 6) 769 -785
151
2012
Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants
Laura Emery , Simon Whelan , Kendal D. Hirschi , Jon K. Pittman
Frontiers in Plant Science 3 1 -1
819
2012
Inferring Trees
Simon Whelan
Bioinformatics 287 -309
11
2008
The genetic code can cause systematic bias in simple phylogenetic models
Simon Whelan
Philosophical Transactions of the Royal Society B 363 ( 1512) 4003 -4011
10
2008
Covariation is a poor measure of molecular coevolution
David Talavera , Simon C. Lovell , Simon Whelan
Molecular Biology and Evolution 32 ( 9) 2456 -2468
40
2015
The prevalence of multifurcations in tree-space and their implications for tree-search
Simon Whelan , Daniel Money
Molecular Biology and Evolution 27 ( 12) 2674 -2677
15
2010
Determination and validation of principal gene products
Michael L. Tress , Jan-Jaap Wesselink , Adam Frankish , Gonzalo López
Bioinformatics 24 ( 1) 11 -17
21
2008
Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable.
Ceferino Varón-González , Simon Whelan , Christian Peter Klingenberg
Systematic Biology 69 ( 5) 863 -883
4
2020
Characterizing the Phylogenetic Tree-Search Problem
Daniel Money , Simon Whelan
Systematic Biology 61 ( 2) 228 -239
19
2012
ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.
Simon Whelan , James E. Allen , Benjamin P. Blackburne , David Talavera
Systematic Biology 64 ( 1) 42 -55
40
2015
GeLL: a generalized likelihood library for phylogenetic models
Daniel Money , Simon Whelan
Bioinformatics 31 ( 14) 2391 -2393
2015
Determining the evolutionary history of gene families
Ryan M. Ames , Daniel Money , Vikramsinh P. Ghatge , Simon Whelan
Bioinformatics 28 ( 1) 48 -55
28
2012
Assessing the state of substitution models describing noncoding RNA evolution.
James E. Allen , Simon Whelan
Genome Biology and Evolution 6 ( 1) 65 -75
13
2014
Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty
A.S. Md Mukarram Hossain , Benjamin P. Blackburne , Abhijeet Shah , Simon Whelan
Genome Biology and Evolution 7 ( 8) 2102 -2116
9
2015