J. Felsenstein

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A primer of population biology

J. Felsenstein, 1972 .

Evolutionary trees from DNA sequences: A maximum likelihood approach

J. Felsenstein, 2005, Journal of Molecular Evolution.

A Pain in the Torus: Some Difficulties with Models of Isolation by Distance

J. Felsenstein, 1975, The American Naturalist.

The theoretical population genetics of variable selection and migration.

J. Felsenstein, 1976, Annual review of genetics.

A Hidden Markov Model approach to variation among sites in rate of evolution.

J. Felsenstein, G. Churchill, 1996, Molecular biology and evolution.

Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods.

J. Felsenstein, 1996, Methods in enzymology.

Inching toward reality: An improved likelihood model of sequence evolution

J. Felsenstein, H. Kishino, J. Thorne, 2004, Journal of Molecular Evolution.

An evolutionary model for maximum likelihood alignment of DNA sequences

J. Felsenstein, H. Kishino, J. Thorne, 1991, Journal of Molecular Evolution.

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.

J. Felsenstein, M. Kuhner, 1994, Molecular biology and evolution.

Maximum likelihood estimation of recombination rates from population data.

Jon A Yamato, J. Felsenstein, M. Kuhner, 2000, Genetics.

Phylogenies and the Comparative Method

J. Felsenstein, 1985, The American Naturalist.

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

J. Felsenstein, 1985, Evolution; international journal of organic evolution.

Numerical Methods for Inferring Evolutionary Trees

J. Felsenstein, 1982, The Quarterly Review of Biology.

Phylogenies from molecular sequences: inference and reliability.

J. Felsenstein, 1988, Annual review of genetics.

Cases in which Parsimony or Compatibility Methods will be Positively Misleading

J. Felsenstein, 1978 .

Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.

Jon A Yamato, J. Felsenstein, M. Kuhner, 1995, Genetics.

Maximum-likelihood estimation of evolutionary trees from continuous characters.

J. Felsenstein, 1973, American journal of human genetics.

Invariants of phylogenies in a simple case with discrete states

J. Felsenstein, J. A. Cavender, 1987 .

An alternating least squares approach to inferring phylogenies from pairwise distances.

J. Felsenstein, 1997, Systematic biology.

EVOLUTIONARY TREES FROM GENE FREQUENCIES AND QUANTITATIVE CHARACTERS: FINDING MAXIMUM LIKELIHOOD ESTIMATES

J. Felsenstein, JOSEPH FELSENSTEIN, 1981, Evolution; international journal of organic evolution.

Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?

J. Felsenstein, 2006, Molecular biology and evolution.

Computational Molecular Evolution.Oxford Series in Ecology and Evolution.ByZiheng Yang. Oxford and New York: Oxford University Press. $115.00 (hardcover); $52.50 (paper). xvi + 357 p.; ill.; index. 0‐19‐856699‐9 (hc); 0‐19‐856702‐2 (pb). 2006.

Joseph Felsenstein, J. Felsenstein, 2008 .

The number of evolutionary trees

Joseph Felsenstein, J. Felsenstein, 1978 .

The effect of assortative mating on the genetic composition of a population.

J. Felsenstein, J. Crow, James F. Crow, 1968, Eugenics quarterly.

Confidence Limits on Phylogenies With a Molecular Clock

J. Felsenstein, 1985 .

Comparative Methods with Sampling Error and Within‐Species Variation: Contrasts Revisited and Revised

J. Felsenstein, 2008, The American Naturalist.

PhyloSift: phylogenetic analysis of genomes and metagenomes

Henry C. M. Leung, Brian C. Thomas, Ocn, 2014, PeerJ.

The evolutionary advantage of recombination.

J. Felsenstein, 1974, Genetics.

SKEPTICISM TOWARDS SANTA ROSALIA, OR WHY ARE THERE SO FEW KINDS OF ANIMALS?

J. Felsenstein, 1981, Evolution; international journal of organic evolution.

Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

Joseph Felsenstein, J. Felsenstein, 1973 .

DISTANCE METHODS FOR INFERRING PHYLOGENIES: A JUSTIFICATION

Joseph Felsenstein, J. Felsenstein, 1984, Evolution; international journal of organic evolution.

Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach

Peter Beerli, Joseph Felsenstein, J. Felsenstein, 2001, Proceedings of the National Academy of Sciences of the United States of America.

The effect of linkage on directional selection.

J. Felsenstein, J Felsenstein, 1965, Genetics.

Parsimony in Systematics: Biological and Statistical Issues

Joseph Felsenstein, J. Felsenstein, 1983 .

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

Alexandros Stamatakis, Adam D. Leaché, Joseph Felsenstein, 2015, Systematic biology.

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences.

David Bryant, Remco Bouckaert, Joseph Felsenstein, 2009, Molecular phylogenetics and evolution.

Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method.

J. Felsenstein, J Felsenstein, 1992, Genetical research.

Methods for Inferring Phylogenies: A Statistical View

J. Felsenstein, 1983 .

Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull

Joseph Felsenstein, Hirohisa Kishino, J. Felsenstein, 1993 .

Usefulness of single nucleotide polymorphism data for estimating population parameters.

Jon A Yamato, J. Felsenstein, M. Kuhner, 2000, Genetics.

On the Biological Significance of the Cost of Gene Substitution

Joseph Felsenstein, J. Felsenstein, 1971, The American Naturalist.

The troubled growth of statistical phylogenetics.

J. Felsenstein, 2001, Systematic biology.

Macroevolution in a Model Ecosystem

Joseph Felsenstein, J. Felsenstein, 1978, The American Naturalist.

Inbreeding and variance effective numbers in populations with overlapping generations.

J. Felsenstein, J Felsenstein, 1971, Genetics.

Using the quantitative genetic threshold model for inferences between and within species

Joseph Felsenstein, J. Felsenstein, 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

How can we infer geography and history from gene frequencies?

J. Felsenstein, J Felsenstein, Joseph Felsenstein, 1982, Journal of theoretical biology.

THE QUARTERLY REVIEW

J. Felsenstein, 1982 .

A Comparative Method for Both Discrete and Continuous Characters Using the Threshold Model

Joseph Felsenstein, J. Felsenstein, 2011, The American Naturalist.

Population genetics and ecology

S. Karlin, J. Felsenstein, E. Nevo, 1976 .

Isolation by distance in a hierarchically clustered population

J. Felsenstein, S. Sawyer, 1983, Journal of Applied Probability.

The American Society of Naturalists Phylogenies and the Comparative Method

J. Felsenstein, 2008 .

A two-stage pruning algorithm for likelihood computation for a population tree.

E. Thompson, J. Felsenstein, A. Roychoudhury, 2008, Genetics.

Population genetics and ecology

S. Karlin, J. Felsenstein, E. Nevo, 1976 .

WAITING FOR POST-NEO-DARWIN.

J. Felsenstein, 1986, Evolution; international journal of organic evolution.

Statistical inference of phylogenies

Joseph Felsenstein, J. Felsenstein, 1983 .

The assessment of population affinities in man

J. Felsenstein, 1973 .

Parsimony in systematics

J. Felsenstein, 1983 .

ANNUAL MEETING SOCIETY FOR THE STUDY OF EVOLUTION

J. Felsenstein, R. Bakker, 1986, Evolution; international journal of organic evolution.

USING THE BOOTSTRAP

J. Felsenstein, 1985 .

Estimation of hominoid phylogeny from a DNA hybridization data set

J. Felsenstein, 2005, Journal of Molecular Evolution.

THE ROBUSTNESS OF HOMOGENEITY TESTS IN 2 X N TABLES.

Joseph Felsenstein, R. Lewontin, J. Felsenstein, 1965 .

PHYLIP: phylogenetic inference package version 3.5c. Distributed over the Internet

J. Felsenstein, J. Felsenstein, 1993 .

Mathematics vs. Evolution: Mathematical Evolutionary Theory.

J. Felsenstein, J Felsenstein, 1989, Science.

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM‐LIKELIHOOD APPROACH

Joseph Felsenstein, J. Felsenstein, 1992, Evolution; international journal of organic evolution.

The evolutionary advantage of recombination. II. Individual selection for recombination.

J. Felsenstein, J Felsenstein, S Yokoyama, 1976, Genetics.

Maximum likelihood estimation of population growth rates based on the coalescent.

Jon A Yamato, J. Felsenstein, M. Kuhner, 1998, Genetics.

Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates.

J. Felsenstein, J Felsenstein, 1992, Genetical research.

Taking Variation of Evolutionary Rates Between Sites into Account in Inferring Phylogenies

Joseph Felsenstein, J. Felsenstein, 2001, Journal of Molecular Evolution.

Counting phylogenetic invariants in some simple cases.

J. Felsenstein, J Felsenstein, J. Felsenstein, 1991, Journal of theoretical biology.

DISTANCE METHODS: A REPLY TO FARRIS

J. Felsenstein, 1986, Cladistics : the international journal of the Willi Hennig Society.

Book Review

J. Felsenstein, 1980, IEEE Transactions on Reliability.

OF VARIABLE SELECTION AND MIGRATION

J. Felsenstein, 1976 .

Phylogenies and quantitative characters

J. Felsenstein, 1988 .

Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.

J. Felsenstein, P. Beerli, J Felsenstein, 1999, Genetics.

A maximum likelihood approach to the detection of selection from a phylogeny

Brian Golding, J. Felsenstein, B. Golding, 1990, Journal of Molecular Evolution.

Biological and Statistical Issues

J. Felsenstein, 2016 .

Likelihoods on coalescents: a Monte Carlo sampling approach to inferring parameters from population samples of molecular data

Peter Beerli, Joseph Felsenstein, Mary K. Kuhner, 1999 .

The occurrence of new mutants in the X-linked recessive Lesch-Nyhan disease.

B. Migeon, J. Felsenstein, U. Francke, 1976, American journal of human genetics.

Excursions along the Interface between Disruptive and Stabilizing Selection.

J. Felsenstein, J. Felsenstein, 1979, Genetics.

Coalescents, Phylogenies, and Likelihoods.

J. Felsenstein, 1999, The Biological Bulletin.

The rate of loss of multiple alleles in finite haploid populations.

J. Felsenstein, 1971, Theoretical population biology.

Statistical phylogeography: Migrate-N, IMa, and ABC

J. Felsenstein, 2018 .

Controlling for non-independence in comparative analysis of patterns across populations within species

Joseph Felsenstein, Sean Nee, J. Felsenstein, 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

Linkage and selection: theoretical analysis of the deterministic two locus random mating model.

W F Bodmer, J. Felsenstein, W. Bodmer, 1967, Genetics.

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

J. Felsenstein, M. Steel, T. Stadler, 2018, bioRxiv.

Sampling among haplotype resolutions in a coalescent‐based genealogy sampler

J. Felsenstein, M. Kuhner, 2000, Genetic Epidemiology.

1 TREES OF GENES IN POPULATIONS

J. Felsenstein, 2022 .

Phylogenies from Gene Frequencies: A Statistical Problem

J. Felsenstein, 1985 .

Isolation by distance: reply to Lalouel and Morton

J. Felsenstein, 1979, Annals of human genetics.

An efficient method for matching nucleic acid sequences

Joseph Felsenstein, Stanley Sawyer, Rochelle Kochin, 1982, Nucleic Acids Res..

10. The Statistical Approach to Inferring Evolutionary Trees and What It Tells Us About Parsimony and Compatibility

J. Felsenstein, 1984 .

Covariation of gene frequencies in a stepping-stone lattice of populations1

J. Felsenstein, 2014, Theoretical population biology.

Estimators of the human effective sex ratio detect sex biases on different timescales.

J. Felsenstein, J. Akey, L. Emery, 2010, American journal of human genetics.

A likelihood approach to character weighting and what it tells us about parsimony and compatibility

Joseph Felsenstein, J. Felsenstein, 1981 .

Population Differences in Quantitative Characters and Gene Frequencies: A Comment on Papers by Lewontin and Rogers

J. Felsenstein, 1986, The American Naturalist.

Evolution in the twentieth century

J. Felsenstein, Joe Felsenstein, 1986, Nature.

THE TOPOLOGY-DEPENDENT PERMUTATION TEST FOR MONOPHYLY DOES NOT TEST FOR MONOPHYLY

David L. Swofford, Jeffrey L. Thorne, Joseph Felsenstein, 1996 .

Access to theory

Joe Felsenstein, J. Felsenstein, 1987, Nature.

A model of kin selection for an altruistic trait considered as a quantitative character.

J. Felsenstein, S. Yokoyama, J. Felsenstein, 1978, Proceedings of the National Academy of Sciences of the United States of America.

The effect of assortative mating on the genetic composition of a population.

J. Felsenstein, J. Crow, 1982, Social biology.

Applications of Metropolis-Hastings Genealogy Sampling

J. Felsenstein, M. Kuhner, J. Yamato, 1997 .

Continuous-genotype models and assortative mating

J. Felsenstein, 1981 .

Alternative Methods of Phylogenetic Inference and their Interrelationship

Joseph Felsenstein, J. Felsenstein, 1979 .

J. Felsenstein, J. Felsenstein, 1974, Genetical research.

A mathematically tractable family of genetic mapping functions with different amounts of interference.

J. Felsenstein, 1979, Genetics.

Quantitative characters, phylogenies, and morphometrics

J. Felsenstein, 2002 .

r- and K-Selection in a Completely Chaotic Population Model

J. Felsenstein, 1979, The American Naturalist.

Bibliography of theoretical population genetics

Joseph Felsenstein, J. Felsenstein, B. Taylor, 1981 .

Probability models and statistical methods in genetics

J. Felsenstein, 1972 .

SKEPTICISM TOWARDS SANTA ROSALIA, OR WHY ARE THERE SO FEW KINDS OF ANIMALS?

J. Felsenstein, 1981, Evolution; international journal of organic evolution.

Parsimony and likelihood: an exchange

Joseph Felsenstein, Elliott Sober, E. Sober, 1986 .

A continuous migration model with stable demography

J. Felsenstein, S. Sawyer, Joseph Felsenstein, 1981, Journal of mathematical biology.

[Statistical Analysis of Hominoid Molecular Evolution]: Comment

J. Felsenstein, 1987 .

A view of population genetics.

J. Felsenstein, 1980, Science.

Exact coalescent likelihoods for unlinked markers in finite-sites mutation models

N. Rosenberg, J. Felsenstein, R. Bouckaert, 2011, 1109.3525.