Molecular phylogenetics: state-of-the-art methods for looking into the past

Trends in Genetics : TIG
S WhelanNick Goldman

Abstract

As the amount of molecular sequence data in the public domain grows, so does the range of biological topics that it influences through evolutionary considerations. In recent years, a number of developments have enabled molecular phylogenetic methodology to keep pace. Likelihood-based inferential techniques, although controversial in the past, lie at the heart of these new methods and are producing the promised advances in the understanding of sequence evolution. They allow both a wide variety of phylogenetic inferences from sequence data and robust statistical assessment of all results. It cannot remain acceptable to use outdated data analysis techniques when superior alternatives exist. Here, we discuss the most important and exciting methods currently available to the molecular phylogeneticist.

References

Jun 1, 1992·Computer Applications in the Biosciences : CABIOS·D T JonesJ M Thornton
Nov 10, 1988·Nature·M A SteelD Penny
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jan 1, 1982·Journal of Molecular Evolution·W M BrownA C Wilson
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Sep 1, 1994·Molecular Phylogenetics and Evolution·M Schöniger, A von Haeseler
Feb 1, 1993·Journal of Molecular Evolution·N Goldman
Jan 1, 1995·Molecular Biology and Evolution·B S Gaut, P O Lewis
Jul 1, 1994·Journal of Molecular Evolution·Z Yang
Jul 1, 1995·Protein Engineering·J M Koshi, R A Goldstein
Apr 1, 1996·Journal of Molecular Evolution·J Adachi, M Hasegawa
May 1, 1996·Journal of Molecular Evolution·Z Yang
May 1, 1996·Molecular Biology and Evolution·J L ThorneD T Jones
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·A Rambaut, N C Grassly
Jul 1, 1997·Molecular Biology and Evolution·Z Yang, B Rannala
Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·N C GrasslyA Rambaut
Apr 29, 1998·Journal of Molecular Evolution·Z Yang, R Nielsen
Oct 27, 1998·Proceedings. Biological Sciences·N Goldman
Dec 29, 1998·Molecular Biology and Evolution·Z YangM Hasegawa
Dec 29, 1998·Molecular Biology and Evolution·J L ThorneI S Painter
Jan 5, 1999·Genome Research·P Liò, N Goldman
Aug 26, 1999·Trends in Genetics : TIG·J S ShoemakerB S Weir
Dec 22, 1999·Molecular Biology and Evolution·P Liò, N Goldman
Feb 10, 2000·Molecular Biology and Evolution·W J BrunoA L Halpern
May 11, 2000·Proceedings of the National Academy of Sciences of the United States of America·J G BishopT Mitchell-Olds
Jun 1, 2000·Molecular Biology and Evolution·M Steel, D Penny
Jun 27, 2000·Bioinformatics·T Massingham, N Goldman
Aug 26, 2000·Molecular Biology and Evolution·S Ota, W H Li
Nov 23, 2000·Current Opinion in Genetics & Development·J L Thorne

❮ Previous
Next ❯

Citations

Sep 27, 2002·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Mikhail V MatzSergey A Lukyanov
Jan 21, 2011·Archives of Microbiology·Roy D Sleator
Dec 14, 2007·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Michaela MarkovaJitka Zluvova
Apr 3, 2004·Trends in Microbiology·Pietro Liò, Nick Goldman
Nov 8, 2003·Gene·Pietro Liò, Marina Vannucci
Mar 15, 2002·Trends in Biochemical Sciences·David S HornerT Martin Embley
Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·G A LunterJ Hein
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Adam Siepel, David Haussler
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Fereydoun HormozdiariArtem Cherkasov
Oct 31, 2008·Briefings in Bioinformatics·Wayne DelportCathal Seoighe
Aug 23, 2008·Bioinformatics·Le Si QuangNicolas Lartillot
May 27, 2008·Molecular Biology and Evolution·Simon Whelan
Jun 28, 2008·Molecular Biology and Evolution·Antonis Rokas, Sean B Carroll
Sep 9, 2008·Molecular Biology and Evolution·Ignacio LuqueJesús A G Ochoa de Alda
Oct 2, 2009·Molecular Biology and Evolution·Jared L Strasburg, Loren H Rieseberg
Jul 10, 2010·Molecular Biology and Evolution·Jennifer Ripplinger, Jack Sullivan
Jul 31, 2010·Molecular Biology and Evolution·Zheng ZhangPeiji Gao
Aug 3, 2013·Molecular Biology and Evolution·Nicola De MaioCarolin Kosiol
Mar 11, 2003·Nucleic Acids Research·C E BullerwellB F Lang
Sep 28, 2004·Nucleic Acids Research·Jakob Skou PedersenJotun Hein
Sep 25, 2002·Molecular Biology and Evolution·Frédéric DelsucEmmanuel J P Douzery
Nov 2, 2002·Molecular Biology and Evolution·Nick Goldman, Simon Whelan
Feb 28, 2002·Molecular Biology and Evolution·Nathan LoClaudio Bandi
Feb 28, 2002·Molecular Biology and Evolution·María Silvina FornasariJulian Echave
May 29, 2002·Molecular Biology and Evolution·Maria AnisimovaZiheng Yang
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Simon Whelan
Oct 6, 2009·Genome Research·Adam Siepel
Apr 3, 2004·Genome Research·Michael I Jensen-SeamanHoward J Jacob
Apr 3, 2004·Genome Research·Kateryna D MakovaFrancesca Chiaromonte
Jan 7, 2004·BMC Bioinformatics·Andrew ButterfieldGavin A Huttley
Apr 5, 2005·BMC Bioinformatics·Gerton LunterJotun Hein
Oct 9, 2007·BMC Bioinformatics·Xiaodan FanJun S Liu
Apr 15, 2008·BMC Bioinformatics·Janis DingelJakob C Mueller

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.