GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution

BMC Genomics
Emmanuel Noutahi, Nadia El-Mabrouk

Abstract

Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process. We describe GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns optimal solutions according to a measure combining both tree likelihood (according to sequence evolution) and a reconciliation score under the Duplication-Transfer-Loss (DTL) model. It can either be used to construct a gene tree from scratch or to correct trees infered by existing reconstruction method, making it highly flexible to various input data types. The method is based on a genetic algorithm acting on a population of trees at each step. It substantially increases the efficiency of the phylogeny space exploration, reducing the risk of falling into local minima, at a reasonable computational time. We have applied GATC to a dataset of simulated cyanobacterial phylogenies, as well as to an empirical dataset of three reference gene families, and showed that it is able to improve gene tree reconstructions compared with...Continue Reading

Associated Datasets

References

Jun 1, 1992·Computer Applications in the Biosciences : CABIOS·D T JonesJ M Thornton
Jan 1, 1984·Journal of Molecular Evolution·C LanaveG Serio
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Aug 1, 1996·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·A EngertV Diehl
Jul 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·L Zhang
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·K ChenM Farach-Colton
Oct 25, 2001·Journal of Molecular Evolution·K KatohT Miyata
Jun 25, 2002·Systematic Biology·Hidetoshi Shimodaira
Jul 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alan R Lemmon, Michel C Milinkovitch
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 26, 2009·BMC Bioinformatics·Simon PenelGuy Perrière
Jun 19, 2009·Bioinformatics·Nicolas LartillotSamuel Blanquart
Jul 28, 2010·Molecular Biology and Evolution·Matthew D Rasmussen, Manolis Kellis
Aug 19, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Y OvadiaR Libeskind-Hadas
Jan 15, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ali TofighJens Lagergren
Jul 9, 2011·Briefings in Bioinformatics·Brigitte BoeckmannChristophe Dessimoz
May 30, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Zhi-Zhong ChenLusheng Wang
Sep 6, 2012·Systematic Biology·Yi-Chieh WuManolis Kellis
Nov 8, 2012·Genome Research·Bastien BoussauVincent Daubin
Apr 10, 2013·Algorithms for Molecular Biology : AMB·Thi Hau NguyenVincent Berry
Aug 9, 2013·Systematic Biology·Gergely J SzöllõsiVincent Daubin
Nov 7, 2013·Nucleic Acids Research·Fabian SchreiberAlex Bateman
Feb 25, 2014·Systematic Biology·Joel SjöstrandJens Lagergren
Jul 30, 2014·Systematic Biology·Gergely J SzöllősiBastien Boussau
Dec 7, 2014·Bioinformatics·Mukul S BansalManolis Kellis
Jul 3, 2015·Genome Biology and Evolution·Brigitte BoeckmannUNKNOWN Quest for Orthologs Species Tree Working Group
May 7, 2016·Bioinformatics·Edwin JacoxCeline Scornavacca
Aug 12, 2016·PloS One·Emmanuel NoutahiEric Tannier

❮ Previous
Next ❯

Software Mentioned

HOGENOM
TreeBeST
PhyloBayes
mt
SPIMAP
DLTRS
PrIME
Giga
ProfileNJ
- DTL

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.