Cargando…

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

BACKGROUND: Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for processes of gene evolution, such as gene duplication and loss, incomplete lineage...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bansal, Mukul S, Burleigh, J Gordon, Eulenstein, Oliver
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2010
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009515/ https://www.ncbi.nlm.nih.gov/pubmed/20122216 http://dx.doi.org/10.1186/1471-2105-11-S1-S42

Ejemplares similares

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
por: Chaudhary, Ruchi, et al.
Publicado: (2012)

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model
por: Markin, Alexey, et al.
Publicado: (2021)

Consensus properties for the deep coalescence problem and their application for scalable tree search
por: Lin, Harris T, et al.
Publicado: (2012)

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
por: Wu, Yi-Chieh, et al.
Publicado: (2014)

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
por: Górecki, Pawel, et al.
Publicado: (2011)

The multiple gene duplication problem revisited
por: Bansal, Mukul S., et al.
Publicado: (2008)

Robinson-Foulds Supertrees
por: Bansal, Mukul S, et al.
Publicado: (2010)

An ILP solution for the gene duplication problem
por: Chang, Wen-Chieh, et al.
Publicado: (2011)

Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model
por: Mawhorter, Ross, et al.
Publicado: (2019)

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
por: Bansal, Mukul S., et al.
Publicado: (2012)

PhyloFinder: An intelligent search engine for phylogenetic tree databases
por: Chen, Duhong, et al.
Publicado: (2008)

An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference
por: Bouckaert, Remco R
Publicado: (2022)

iGTP: A software package for large-scale gene tree parsimony analysis
por: Chaudhary, Ruchi, et al.
Publicado: (2010)

On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model
por: Bork, Daniel, et al.
Publicado: (2017)

Triplet supertree heuristics for the tree of life
por: Lin, Harris T, et al.
Publicado: (2009)

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species
por: Rogers, Jennifer, et al.
Publicado: (2017)

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation
por: Kundu, Soumya, et al.
Publicado: (2018)

Efficient Bayesian inference under the structured coalescent
por: Vaughan, Timothy G., et al.
Publicado: (2014)

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
por: Górecki, Pawel, et al.
Publicado: (2012)

Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent
por: Lohse, Konrad, et al.
Publicado: (2016)

Efficient Bayesian inference under the multispecies coalescent with migration
por: Flouri, Tomáš, et al.
Publicado: (2023)

Improved Heuristics for Minimum-Flip Supertree Construction
por: Chen, Duhong, et al.
Publicado: (2007)

Rooting phylogenetic trees under the coalescent model using site pattern probabilities
por: Tian, Yuan, et al.
Publicado: (2017)

Linear-time algorithms for phylogenetic tree completion under Robinson–Foulds distance
por: Bansal, Mukul S.
Publicado: (2020)

Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
por: Rannala, Bruce, et al.
Publicado: (2017)

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss
por: Bansal, Mukul S, et al.
Publicado: (2018)

Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
por: Tiley, George P, et al.
Publicado: (2018)

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling
por: Gerard, David, et al.
Publicado: (2011)

Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent
por: Flouri, Tomáš, et al.
Publicado: (2022)

Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
por: Tiley, George P., et al.
Publicado: (2016)

Phylogenetic diversity statistics for all clades in a phylogeny
por: Grover, Siddhant, et al.
Publicado: (2023)

Species Tree Inference by Minimizing Deep Coalescences
por: Than, Cuong, et al.
Publicado: (2009)

Correction to: Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent
Publicado: (2022)

Duplications and losses in gene families of rust pathogens highlight putative effectors
por: Pendleton, Amanda L., et al.
Publicado: (2014)

ASTRAL: genome-scale coalescent-based species tree estimation
por: Mirarab, S., et al.
Publicado: (2014)

A coalescence of two syndromes in a girl with terminal deletion and inverted duplication of chromosome 5
por: Krgovic, Danijela, et al.
Publicado: (2014)

Exact median-tree inference for unrooted reconciliation costs
por: Górecki, Paweł, et al.
Publicado: (2020)

Complex Population Dynamics and the Coalescent Under Neutrality
por: Volz, Erik M.
Publicado: (2012)

In the light of deep coalescence: revisiting trees within networks
por: Zhu, Jiafan, et al.
Publicado: (2016)

Statistical inconsistency of the unrooted minimize deep coalescence criterion
por: Alanzi, Ayed A. R., et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_oribiv0ikp86l2toekc7ucoa1a