In subdirectory invariants:
Felsenstein, J. 1990. Counting phylogenetic invariants in some simple cases. Journal of Theoretical Biology 152: 357-376.
In subdirectory restml:
Felsenstein, J. 1992. Phylogenies from restriction sites: a maximum likelihood approach. Evolution 46: 159-173.
In subdirectory ne:
Felsenstein, J. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research 59: 139-147.
In subdirectory montecarlo:
Felsenstein, J. 1992. Estimating effective population size from population samples of sequences: a bootstrap Monte Carlo approach. Genetical Research 59: 139-147 (December issue).
[note -- the method proposed in this paper is wrong. It has been shown to give a biased estimate of theta. The paper by Felsenstein, Yamato, and Kuhner corrects this. That paper is available here in directory http://evolution.gs.washington.edu/papers/metro and the program to implement it is the LAMARC package.
In subdirectory hillis:
Felsenstein, J. and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42: 193-200 (June)
In subdirectory simulation:
Kuhner, M. K. and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11: 459-468.
In subdirectory metro:
Kuhner, M. K., J. Yamato, and J. Felsenstein. 1995. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
In subdirectory hmc:
Felsenstein, J. and G. A. Churchill. 1996. A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution. Molecular Biology and Evolution 13: 93-104.
In subdirectory proteins:
Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. pp. 418-427 in "Computer Methods for Macromolecular Sequence Analysis," ed. R. F. Doolittle. Methods in Enzymology, vol. 266. Academic Press, Orlando, Florida.
In subdirectory ima:
Kuhner, M. K., J. Yamato, and J. Felsenstein 1997. Applications of Metropolis-Hastings genealogy sampling. pp. 183-192 in "Progress in Population Genetics and Human Evolution", ed. P. Donnelly and S. Tavare. IMA Volumes in Mathematics and its Applications, volume 87. Springer Verlag, Berlin.
In subdirectory distance
Felsenstein, J. 1997. An alternating least squares approach to inferring phylogenies from pairwise distances. Systematic Biology 46: 101-111.
In subdirectory migrate
Beerli, P. and J. Felsenstein. 1999. Maximum Likelihood estimation of migration rates and effective population numbers in two populations. Genetics 152: 763-773.
In subdirectory ims
Felsenstein, J., M. K. Kuhner, J. Yamato, and P. Beerli. 1999. Likelihoods on coalescents: a Monte Carlo sampling approach to inferring parameters from population samples of molecular data. pp. 163-185 in "Statistics in Molecular Biology and Genetics", ed. Francoise Seillier-Moiseiwitsch. IMS Lecture Notes-Monograph Series, volume 33. Institute of Mathematical Statistics and American Mathematical Society, Hayward, California.
In subdirectory evolgen
Felsenstein, J. 2000. From population genetics to evolutionary genetics: a view through the trees. pp. 609-627 in "Evolutionary Genetics: From Molecules to Morphology", ed. R. S. Singh and C. B. Krimbas. Cambridge University Press, Cambridge.
In subdirectory snp
Kuhner, M. K., P. Beerli, J. Yamato, and J. Felsenstein. 2000. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156: 439-447.
In subdirectory statphyl
Felsenstein, J. 2001. The troubled growth of statistical phylogenetics. Systematic Biology 50: 465-467.
In subdirectory rates
Felsenstein, J. 2001. Taking variation of evolutionary rates between sites into account in inferring phylogenies. Journal of Molecular Evolution 53: 447-455.
In subdirectory quantchar
Felsenstein, J. 2002. Quantitative characters, phylogenies, and morphometrics.pp. 27-44 in "Morphology, Shape, and Phylogenetics", ed. N. MacLeod. Systematics Association Special Volume Series 64. Taylor and Francis, London.
In subdirectory spectrum
Felsenstein, J. 2002. Contrasts for a within-species comparative method. pp. 118-129 in "Modern Developments in Theoretical Population Genetics", ed. M. Slatkin and M. Veuille. Oxford University Press, Oxford.
In subdirectory galton
Felsenstein, J. 2004. An ancestor's influence (review of "Francis Galton: Pioneer of Heredity and Biometry", by Michael Bulmer). Nature Genetics 36 (10): 1031.
In subdirectory threshold
Felsenstein, J. 2005. Using the quantitative genetic threshold model for inferences between and within species. Philosophical Transactions of the Royal Society of London, series B 360: 1427-1434.
In subdirectory coalpower
Felsenstein, J. 2006. Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci? Molecular Biology and Evolution 23: 691-700.
In subdirectory paris2005
Felsenstein, J. 2007. Trees of genes in populations. pp. 3-29 in "Reconstructing Evolution. New Mathematical and Computational Advances", ed. Olivier Gascuel and Mike Steel. Clarendon Press, Oxford.
In subdirectory comparerr
Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171: 713-725.
In subdirectory stone
Stone, G. N., S. Nee, and J. Felsenstein. 2011. Controlling for non-independence in comparative analysis of patterns across populations within species. Philosophical Transactions of the Royal Society B 366 (1569): 1410-1424.
In subdirectory threshold2
Felsenstein, J. 2012. A comparative method for both discrete and continuous characters using the threshold model. American Naturalist 179: 145-156.
Please note carefully that these papers, as published in the journals, are copyright to the publishers of those journals.
Note that in each case these are the final versions as submitted to the journal (the last full manuscript version) but do not reflect changes that the editor or I may have made in proof. Published quotations of these manuscripts should be based on the published version; quotations before publication should be checked with me by e-mail.
In addition, many of my older papers are available on-line in the JSTOR system which makes older academic journals available. Your institution would need to have a subscription to JSTOR for it to be available to you. Links to these papers are available in my Curriculum Vitae which is at this link. It also has links to on-line copies of some of my papers at the sites of the journals that published them. These too may require subscriptions.
joe (at) gs.washington.edu