Webserver citations. If you publish the results based on Datamonkey.org we suggest the following citations. Please cite the Datamonkey and HyPhy application notes:

Datamonkey webserver

Wayne Delport, Art F. Poon, Simon D. W. Frost and Sergei L. Kosakovsky Pond
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
Bioinformatics 2010 July 29[Epub ahead of print; PMID: 20671151]

Sergei L. Kosakovsky Pond and Simon D. W. Frost (2005)
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
Bioinformatics 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 21(5): 676-679

Method citations. Please also cite the appropriate methods paper for the analyses you have used:

MEME

Ben Murrell, Joel O. Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, Sergei L. Kosakovsky Pond (2012)
Detecting Individual Sites Subject to Episodic Diversifying Selection
PLoS Genetics 8(7): e1002764

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 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 2(6): e62

TOGGLE

Wayne Delport, Konrad Scheffler and Cathal Seoighe (2008)
Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1
PLoS Pathogens 4(12): e1000242

DEPS

Sergei L Kosakovsky Pond, Art FY Poon, Andrew J Leigh Brown and Simon Frost (2008)
A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus
Molecular Biology and Evolution 25(9): 1809-1824

PARRIS

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

GA-Branch

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

ESD

Sergei L Kosakovsky Pond, Konrad Scheffler, Michael B Gravenor, Art FY Poon and Simon DW Frost (2009)
Evolutionary Fingerprinting of Genes
Molecular Biology and Evolution 27(3): 520-536

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 Computational Biology 3(11): e23

CMS

Wayne Delport, Konrad Scheffler, Gordon Botha, Michael B Gravenor, Spencer V. Muse and Sergei L Kosakovsky Pond (2010)
CodonTest: modeling amino-acid substitution preferences in coding sequences
PLoS Computational Biology 6(8): e1000885

Branch-site REL and MEME

Sergei L. Kosakovsky Pond1, Ben Murrell, Mathieu Fourment, Simon D. W. Frost, Wayne Delport and Konrad Scheffler (2011)
A random effects branch-site model for detecting episodic diversifying selection
Molecular Biology and Evolution (first published online June 13, 2011 doi:10.1093/molbev/msr125)

SBP/GARD

Sergei L Kosakovsky Pond, David Posada, Michael B Gravenor, Christopher H Woelk and Simon DW Frost
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
Molecular Biology and Evolution 23(10): 1891-1901

SCUEAL

Sergei L Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, Art FY Poon, Gareth Hughes, Esther Fearnhill, Mike B Gravenor, Andrew J Leigh Brown and Simon DW Frost (2009)
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
PLoS Computational Biology 5(11): e1000581

ASR (joint)

Tal Pupko, Itsik Pe'er Ron Shamir and Dan Graur (2000)
A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences
Molecular Biology and Evolution 17: 890-896

ASR (marginal)

Z Yang, S Kumar and M Nei (1995)
A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences
Genetics 141: 1641-1650

ASR (sampled)

Rasmus Nielsen (2002)
Mapping mutations on phylogenies
Systematic Biology 51(5): 729-739