MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

BMC Bioinformatics
Raphaël Helaers, Michel C Milinkovitch

Abstract

The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical use...Continue Reading

References

Apr 1, 1981·AJR. American Journal of Roentgenology·D L Daniels, F E Maddison
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Dec 29, 1998·Molecular Biology and Evolution·J L ThorneI S Painter
Oct 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·I CassensM C Milinkovitch
Oct 25, 2001·Journal of Molecular Evolution·K KatohT Miyata
Apr 27, 2002·Systematic Biology·D R MaddisonW P Maddison
Jul 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alan R Lemmon, Michel C Milinkovitch
Aug 30, 2002·Molecular Biology and Evolution·Belinda S W ChangThomas P Sakmar
Oct 12, 2002·Science·M MeegaskumburaC J Schneider
Oct 25, 2002·Systematic Biology·John P HuelsenbeckFredrik Ronquist
Oct 25, 2002·Systematic Biology·Jeffrey L Thorne, Hirohisa Kishino
Apr 3, 2003·Nature Reviews. Genetics·Mark Holder, Paul O Lewis
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Dec 3, 2003·Toxicology and Applied Pharmacology·James F DillmanJohn J Schlager
Dec 3, 2004·Genome Research·Mathieu BlanchetteDavid Haussler
Jun 18, 2005·Bioinformatics·Benny Chor, Tamir Tuller
May 17, 2006·Trends in Ecology & Evolution·Mark S SpringerWilfried W de Jong
Jun 23, 2006·PLoS Computational Biology·Paul D WilliamsRichard A Goldstein
May 13, 1983·Science·S KirkpatrickM P Vecchi
Mar 18, 2008·Molecular Phylogenetics and Evolution·Wei Zhang, Zhirong Sun
Nov 6, 2008·Genome Biology·Toni Gabaldón
Apr 17, 2009·Bioinformatics·Marc A Suchard, Andrew Rambaut
Sep 1, 1996·Trends in Ecology & Evolution·Z Yang

❮ Previous
Next ❯

Citations

Jan 26, 2013·Genome Biology and Evolution·Urszula BrykczynskaMichel C Milinkovitch
Mar 24, 2012·PloS One·Kevin Liu, Tandy Warnow
Jul 11, 2013·PloS One·Nicholas J KaplinskyRay Watson
Jun 27, 2014·PLoS Genetics·Jung-Ho ShinWade C Winkler
Feb 20, 2014·Developmental and Comparative Immunology·Iván Rodríguez-NunezJeffrey A Yoder
Oct 1, 2014·Proceedings of the National Academy of Sciences of the United States of America·Guillaume CornelisThierry Heidmann
Nov 26, 2015·Critical Reviews in Biochemistry and Molecular Biology·April E RoseChristian Schlieker
Feb 3, 2016·International Journal of Food Microbiology·Morten HertzJens Laurids Sørensen
Nov 29, 2015·Molecular Ecology·J R PrashanthR J Lewis
Sep 10, 2013·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Massimo GiovannottiVincenzo Caputo Barucchi
Jun 7, 2015·Fungal Genetics and Biology : FG & B·Alexander I PutmanIgnazio Carbone
Jul 16, 2013·Bio Systems·Sergio Santander-Jiménez, Miguel A Vega-Rodríguez
Dec 30, 2014·Fungal Genetics and Biology : FG & B·Frederik T HansenJens Laurids Sørensen
Dec 4, 2012·International Journal for Parasitology·Simona GeorgievaAneta Kostadinova
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
May 7, 2016·Molecular Phylogenetics and Evolution·Maximilian A R Strobl, Daniel Barker
Apr 29, 2016·Systematic Biology·Olga ChernomorBui Quang Minh
Jun 18, 2017·Experimental & Applied Acarology·Ricardo García-JiménezAntonio G Valdecasas
Dec 27, 2017·International Journal of Molecular Sciences·Xiaoping MinNingshao Xia
Feb 10, 2018·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Massimo GiovannottiVincenzo Caputo Barucchi
Oct 31, 2018·The Journal of Biological Chemistry·Juan M Adrian-SegarraJochen Pöling
Sep 10, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Birgit LengererPatrick Flammang
Oct 28, 2019·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Jose L HorreoPatrick S Fitze
May 7, 2020·Journal of Bioinformatics and Computational Biology·Yourim Yoon, Yong-Hyuk Kim
Feb 22, 2017·Emerging Infectious Diseases·Sven MalmStefan Niemann
Aug 29, 2018·Viruses·Timo GreinerGerhard Thiel
Aug 1, 2020·Briefings in Bioinformatics·Cátia VazAlexandre P Francisco
Aug 13, 2017·Molecular Plant Pathology·Jens Laurids SørensenDonald Max Gardiner

❮ Previous
Next ❯

Software Mentioned

Nexus
MacOS X
Windows
Linux
metaGA
Garli
Tree Viewer
MetaPIGA
PhyML
RaxML

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.