Suggested citations. If you publish the results based on Datamonkey.org we suggest the following citations. Please cite the Datamonkey and HyPhy application notes and relevant methodology papers.

Datamonkey webserver

Sergei L. Kosakovsky Pond and Simon D. W. Frost (2005)
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
Bioinformatics 2005 21(10):2531-2533

HyPhy package

Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005)
HyPhy: hypothesis testing using phylogenies
Bioinformatics 2005 21(5):676-679

SLAC/FEL/REL

Sergei L. Kosakovsky Pond and Simon D. W. Frost (2005)
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
Molecular Biology and Evolution 2005 22(5):1208-1222

IFEL

Sergei L Kosakovsky Pond, Simon DW Frost, Zehava Grossman, Michael B Gravenor, Douglas D Richman and Andrew J Leigh Brown (2006)
Adaptation to different human populations by HIV-1 revealed by codon-based analyses
PLoS Computational Biology Vol. 2, No. 6, e62

GA-Branch

S.L. Kosakovsky Pond and S.D.W. Frost (2005)
A Genetic Algorithm Approach to Detecting Lineage-specific Variation in Selection Pressure
Mol. Biol. and Evolution 22(3):478-485

PARRIS

Konrad Scheffler,Darren P. Martin and Cathal Seoighe (2006)
Robust inference of positive selection from recombining coding sequences
Bioinformatics 2006 22(20):2493-2499

Spidermonkey/BGM

Art Poon, Fraser Lewis, Sergei Kosakovsky Pond and Simon Frost (2007)
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope
PLoS Comput Biol. 2007 Nov;3(11):e23