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diff --git a/academic/hyphy/References b/academic/hyphy/References new file mode 100644 index 0000000000..0c7b457efe --- /dev/null +++ b/academic/hyphy/References @@ -0,0 +1,28 @@ +HyPhy +Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005) +HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5): 676-679 + +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 + +Specific methods implemented in HyPhy +Selection detection (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 +Internal Fixed Effects Likelihood (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. +Directional Evolution in Protein Sequences (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 +Evolutionary Selection Distance (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 +Codon Model Selection (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 - 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) +MEME - Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., and Kosakovsky Pond, S. L. (2012) Detecting Individual Sites Subject to Episodic Diversifying Selection". PLoS Genet, 8(7), e1002764+ +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 +Ancestral Sequence Reconstruction (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 |