Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees".

Science
Fredrik RonquistPaul van der Mark

Abstract

Mossel and Vigoda (Reports, 30 September 2005, p. 2207) show that nearest neighbor interchange transitions, commonly used in phylogenetic Markov chain Monte Carlo (MCMC) algorithms, perform poorly on mixtures of dissimilar trees. However, the conditions leading to their results are artificial. Standard MCMC convergence diagnostics would detect the problem in real data, and correction of the model misspecification would solve it.

References

Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Dec 18, 2001·Science·J P HuelsenbeckJ P Bollback
Oct 25, 2002·Systematic Biology·John P HuelsenbeckFredrik Ronquist
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Feb 18, 2004·Systematic Biology·Johan A A NylanderJosé Luis Nieves-Aldrey
Nov 5, 2004·Molecular Biology and Evolution·Bret LargetDeborah Sweet
Oct 1, 2005·Science·Elchanan Mossel, Eric Vigoda

❮ Previous
Next ❯

Citations

Dec 8, 2009·Annual Review of Entomology·Fredrik Ronquist, Andrew R Deans
Jul 25, 2008·PLoS Genetics·Aaron E DarlingMark A Ragan
May 17, 2008·International Journal of Plant Genomics·Stéphane Aris-Brosou, Xuhua Xia
Oct 20, 2011·Molecular Biology and Evolution·A M KedzierskaM Casanellas
Apr 24, 2007·The New Phytologist·Mary L Berbee, John W Taylor
Feb 19, 2008·Systematic Biology·Clemens LaknerFredrik Ronquist
Aug 11, 2011·Systematic Biology·Sebastian Höhna, Alexei J Drummond
Mar 8, 2012·American Journal of Botany·Jennifer J PetersenDaniel Potter
Feb 11, 2014·American Journal of Botany·Nancy F Refulio-Rodriguez, Richard G Olmstead
Apr 25, 2008·Systematic Biology·Chris VendittiMark Pagel
Aug 2, 2017·Journal of Mathematical Biology·Alex GavryushkinFrederick A Matsen
Jan 30, 2015·Systematic Biology·Chris Whidden, Frederick A Matsen

❮ 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.