Cargando…

Phylogeny Estimation by Integration over Isolation with Migration Models

Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framewo...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hey, Jody, Chung, Yujin, Sethuraman, Arun, Lachance, Joseph, Tishkoff, Sarah, Sousa, Vitor C, Wang, Yong
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2018
Materias:	Methods
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231491/ https://www.ncbi.nlm.nih.gov/pubmed/30137463 http://dx.doi.org/10.1093/molbev/msy162

Ejemplares similares

Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories
por: Phifer-Rixey, Megan, et al.
Publicado: (2020)

Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations
por: Wang, Shuoguo, et al.
Publicado: (2013)

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
por: Nguyen, Lam-Tung, et al.
Publicado: (2015)

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies
por: Yuan, Ke, et al.
Publicado: (2015)

The Effect of Nonreversibility on Inferring Rooted Phylogenies
por: Cherlin, Svetlana, et al.
Publicado: (2018)

HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
por: Crispell, Joseph, et al.
Publicado: (2019)

Log Transformation Improves Dating of Phylogenies
por: Mai, Uyen, et al.
Publicado: (2020)

Placing Ancient DNA Sequences into Reference Phylogenies
por: Martiniano, Rui, et al.
Publicado: (2022)

Single-cell mutational profiling and clonal phylogeny in cancer
por: Potter, Nicola E., et al.
Publicado: (2013)

Ultra-large alignments using phylogeny-aware profiles
por: Nguyen, Nam-phuong D., et al.
Publicado: (2015)

Contamination detection in sequencing studies using the mitochondrial phylogeny
por: Weissensteiner, Hansi, et al.
Publicado: (2021)

Controls for Phylogeny and Robust Analysis in Pareto Task Inference
por: Adler, Miri, et al.
Publicado: (2021)

PHACT: Phylogeny-Aware Computing of Tolerance for Missense Mutations
por: Kuru, Nurdan, et al.
Publicado: (2022)

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
por: Malikic, Salem, et al.
Publicado: (2019)

Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models
por: Kern, Andrew D., et al.
Publicado: (2017)

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling
por: Hall, Matthew D, et al.
Publicado: (2019)

Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies
por: Didelot, Xavier, et al.
Publicado: (2020)

PhyloMed: a phylogeny-based test of mediation effect in microbiome
por: Hong, Qilin, et al.
Publicado: (2023)

Teaching computational genomics and bioinformatics on a high performance computing cluster—a primer
por: Sethuraman, Arun
Publicado: (2022)

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits
por: Nadeau, Sarah, et al.
Publicado: (2022)

Assessing the impact of recombination on the estimation of isolation-with-migration models using genomic data: a simulation study
por: Chung, Yujin
Publicado: (2023)

Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series
por: Li, Lucy M., et al.
Publicado: (2017)

A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies
por: Tao, Qiqing, et al.
Publicado: (2019)

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees
por: Wang, Yaxuan, et al.
Publicado: (2020)

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia
por: Jones, Matthew G, et al.
Publicado: (2020)

Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
por: Balmori-de la Puente, Alfonso, et al.
Publicado: (2022)

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
por: Kaufmann, Tom L., et al.
Publicado: (2022)

CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
por: Lu, Bingxin, et al.
Publicado: (2023)

Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species
por: Mugal, Carina F, et al.
Publicado: (2020)

Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
por: Bhutkar, Arjun, et al.
Publicado: (2007)

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
por: Gross, Samuel S, et al.
Publicado: (2007)

ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
por: Sashittal, Palash, et al.
Publicado: (2023)

Improved methods for creating migratable Holliday junction substrates
por: Chen, Stefanie Hartman, et al.
Publicado: (2013)

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)
por: Gillett, Conrad P.D.T., et al.
Publicado: (2014)

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
por: Kozlov, Alexey, et al.
Publicado: (2022)

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data
por: Kang, Senbai, et al.
Publicado: (2022)

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
por: Farhat, Maha R, et al.
Publicado: (2014)

Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses
por: Dugourd, Aurelien, et al.
Publicado: (2021)

The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses
por: Webb, Andrew, et al.
Publicado: (2021)

Recent advances in Bayesian inference of isolation-with-migration models
por: Chung, Yujin
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_mgth8i7liuj742ti7dclr1a38o