Citations

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


Datamonkey

Steven Weaver, Stephen D. Shank, Stephanie J. Spielman, Michael Li, Spencer V. Muse, Sergei L. Kosakovsky Pond

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes

Mol. Biol. Evol. 35(3):773–777


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, J. O. Wertheim, S. Weaver, B. Murrell, 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 Pond, 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, S. Weaver, M. D. Smith, J. O. Wertheim, S. Murrell, A. Aylward and K. Eren, T. Pollner, D. P. Martin, D. M. Smith, 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, S. Moola, A. Mabona, T. Weighill, D. Sheward, 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 and Sergei L. Kosakovsky Pond (2012)

Detecting Individual Sites Subject to Episodic Diversifying Selection

PLoS Genetics 8(7): e1002764

RELAX

J. O. Wertheim, B. Murrell, M. D. Smith, 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