Citations

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

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 26(19): 2455-2457

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

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

aBSREL

M. D. Smith and J. O. Wertheim and S. Weaver and B. Murrell and K. Scheffler and S. L. Kosakovsky Pond
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
Molecular Biology and Evolution 32: 1342-1353
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 28(11): 3033-3043

BUSTED

B. Murrell and S. Weaver and M. D. Smith and J. O. Wertheim and S. Murrell and A. Aylward and K. Eren and T. Pollner and D. P. Martin and D. M. Smith and K. Scheffler and S. L. Kosakovsky Pond
Gene-Wide Identification of Episodic Selection
Molecular Biology and Evolution 32(5) 1365-1371

FEL

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

FUBAR

B. Murrell and S. Moola and A. Mabona and T. Weighill and D. Sheward and S. L. Kosakovsky Pond and K. Scheffler
FUBAR: a fast, unconstrained bayesian approximation for inferring selection
Molecular Biology and Evolution 30(5) : 1196-1205

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

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

RELAX

J. O. Wertheim and B. Murrell and M. D. Smith and S. L. Kosakovsky Pond and K. Scheffler
RELAX: detecting relaxed selection in a phylogenetic framework
Molecular Biology and Evolution 32(3): 820-832

SLAC

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