phydms: software for phylogenetic analyses informed by deep mutational scanning

Functional Segregation of Overlapping Genes in HIV

(2016) Jason D. Fernandes et al.   CELL

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

(2016) Michael Doud et al.   Viruses-Basel

Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function

(2016) Parul Mishra et al.   Cell Reports

Phenotypic Characterization of a Comprehensive Set of MAPK1 /ERK2 Missense Mutants

(2016) Lisa Brenan et al.   Cell Reports

Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture

(2016) Hugh K. Haddox et al.   PLoS Pathogens

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

(2016) David Mavor et al.   eLife

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

(2015) Michael B. Doud et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Relationship between dN/dS and Scaled Selection Coefficients

(2015) Stephanie J. Spielman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data

(2014) Asif U. Tamuri et al.   GENETICS

An Experimentally Informed Evolutionary Model Improves Phylogenetic Fit to Divergent Lactamase Homologs

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Comprehensive mutational scanning of a kinasein vivoreveals substrate-dependent fitness landscapes

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

Modeling Evolution Using the Probability of Fixation: History and Implications

(2014) David M. McCandlish et al.   QUARTERLY REVIEW OF BIOLOGY

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

(2013) N. Rodrigue et al.   BIOINFORMATICS

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications

(2012) Toby Kenney et al.   Statistical Applications in Genetics and Molecular Biology

Remark on “algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization”

(2011) José Luis Morales et al.   ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

(2010) Sergei Kosakovsky Pond et al.   PLoS One

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA