A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

Systematic Biology
Stéphane Guindon, Olivier Gascuel


The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences ...Continue Reading


Jul 2, 2004·Molecular Biology and Evolution·Stéphanie BertrandMarc Robinson-Rechavi
Jun 4, 2004·Molecular Biology and Evolution·Hervé PhilippeDidier Casane
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bastien BoussauSiv G E Andersson
Oct 30, 2004·Bioinformatics·T M KeaneG P McCormack
Jun 29, 2005·Journal of Molecular Evolution·Alexandra CalteauGuy Perrière
Jun 29, 2005·Journal of Molecular Evolution·Peng ShiYa-ping Zhang
Aug 13, 2005·Proceedings. Biological Sciences·Michael T MonaghanAlfried P Vogler
Feb 11, 2005·Molecular Biology and Evolution·Hervé PhilippeHenner Brinkmann
Sep 20, 2005·Journal of Molecular Evolution·Patricia Lariguet, Christophe Dunand
Jul 29, 2005·Molecular Biology and Evolution·Jinling HuangJohann Peter Gogarten
May 6, 2005·Nature·Domino A JoyceOle Seehausen
Oct 13, 2005·Development Genes and Evolution·Rebecca F Furlong, Anthony Graham
Jun 17, 2005·The Journal of General Virology·Monique M van OersJust M Vlak
Oct 18, 2005·Proceedings of the National Academy of Sciences of the United States of America·Cheng-Han Huang, Jianbin Peng
Jul 15, 2005·International Journal of Systematic and Evolutionary Microbiology·Martin KoliskoJaroslav Flegr
Dec 7, 2005·Proceedings of the National Academy of Sciences of the United States of America·E F MongodinF Rodriguez-Valera
Sep 30, 2005·Proceedings. Biological Sciences·Charles C DavisKenneth J Wurdack
Feb 17, 2006·PLoS Genetics·Julie C Dunning HotoppHervé Tettelin
Dec 29, 2005·Proceedings of the National Academy of Sciences of the United States of America·Patrick O'DonoghueZaida A Luthey-Schulten
Aug 3, 2006·Molecular Biology and Evolution·Iñaki ComasFernando Gonzalez-Candelas
May 10, 2006·Bioinformatics·Anne-Muriel ArigonManolo Gouy
Jun 21, 2006·Systematic Biology·Maria Anisimova, Olivier Gascuel
Jun 7, 2006·Journal of Molecular Evolution·Jérôme FlakowskiJan Pawlowski
Jul 6, 2006·Development Genes and Evolution·Michaël ManuelHervé Le Guyader
Jun 22, 2006·Molecular Biology and Evolution·Nicolas RodrigueNicolas Lartillot
Aug 1, 2006·Molecular Biology and Evolution·Tetyana NosenkoDebashish Bhattacharya
Nov 1, 2006·Journal of Molecular Evolution·Erick DesmaraisFrançois Bonhomme
Jun 2, 2006·International Journal of Systematic and Evolutionary Microbiology·Sergey I NikolaevJan Pawlowski
Dec 22, 2006·PloS One·Ines Van BocxlaerFranky Bossuyt
Nov 7, 2006·Development Genes and Evolution·Hongyan ShanZheng Meng
Oct 7, 2006·Virus Genes·Alice Kazuko Inoue-NagataTatsuya Nagata

❮ Previous
Next ❯

Related Concepts

Trending Feeds


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 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.


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.