The inference of gene trees with species trees (Q34431226)

2 August 2017

2 references

20 June 2019

19 September 2019

The inference of gene trees with species trees (English)

1 reference

biomedical investigative technique

2 August 2017

1 reference

19 September 2019

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Gergely J Szöllősi

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Vincent Daubin

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

2

Eric Tannier

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

publication date

28 July 2014

1 reference

PubMed ID

25070970

2 August 2017

1 January 2015

2 references

20 June 2019

19 September 2019

3 references

20 June 2019

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

64

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

page(s)

e42-62

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 4.0 International

31 May 2020

copyright license

2 references

20 June 2019

Genome-wide probabilistic reconciliation analysis across vertebrates

19 September 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Gene tree correction guided by orthology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Lateral gene transfer, rearrangement, reconciliation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

DrML: probabilistic modeling of gene duplications

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

FPSAC: fast phylogenetic scaffolding of ancient contigs.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Efficient exploration of the space of reconciled gene trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Evolutionary biochemistry: revealing the historical and physical causes of protein properties.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

STRAW: Species TRee Analysis Web server

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

The zebrafish reference genome sequence and its relationship to the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Improved reversible jump algorithms for Bayesian species delimitation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

The estimation of tree posterior probabilities using conditional clade probability distributions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Lateral gene transfer from the dead

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Systematic inference of highways of horizontal gene transfer in prokaryotes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Genome-scale coestimation of species and gene trees.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

DLRS: gene tree evolution in light of a species tree

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Evolution of gene neighborhoods within reconciled phylogenies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

TreeFix: statistically informed gene tree error correction using species trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Lateral gene transfer as a support for the tree of life

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Modeling gene family evolution and reconciling phylogenetic discord.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Insights into hominid evolution from the gorilla genome sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Bayesian phylogenetics with BEAUti and the BEAST 1.7

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Unified modeling of gene duplication, loss, and coalescence using a locus tree

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Evolution of increased complexity in a molecular machine

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Models, algorithms and programs for phylogeny reconciliation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Reconstructing the architecture of the ancestral amniote genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Guided tree topology proposals for Bayesian phylogenetic inference.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Inference of human population history from individual whole-genome sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

An ILP solution for the gene duplication problem

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Rapid evolutionary innovation during an Archaean genetic expansion.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

iGTP: a software package for large-scale gene tree parsimony analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Inferring the dynamics of diversification: a coalescent approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Inference of homologous recombination in bacteria using whole-genome sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

A Bayesian approach for fast and accurate gene tree reconstruction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Unifying vertical and nonvertical evolution: a stochastic ARG-based framework

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Bayesian species delimitation using multilocus sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Ohnologs in the human genome are dosage balanced and frequently associated with disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogenetic comparative assembly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Isolation with migration models for more than two populations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Bayesian inference of species trees from multilocus data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Genomes as documents of evolutionary history

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Species tree inference by minimizing deep coalescences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Bayesian inference of population size history from multiple loci

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Dynamics of genome rearrangement in bacterial populations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogenetic detection of recombination with a Bayesian prior on the distance between trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Efficient inference of bacterial strain trees from genome-scale multilocus data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Estimating species trees using multiple-allele DNA sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

A model of horizontal gene transfer and the bacterial phylogeny problem

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

High-resolution species trees without concatenation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Discordance of species trees with their most likely gene trees.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogenetic identification of lateral genetic transfer events

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Joint Bayesian Estimation of Alignment and Phylogeny

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Resurrecting ancestral alcohol dehydrogenases from yeast

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Stochastic models for horizontal gene transfer: taking a random walk through tree space

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Cladogenesis, coalescence and the evolution of the three domains of life

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogenetic classification and the universal tree

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Evolutionary trees from DNA sequences: A maximum likelihood approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Phylogenies from molecular sequences: inference and reliability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Bayesian estimation of concordance among gene trees.

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Efficient likelihood computations with nonreversible models of evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Gene tree parsimony vs uninode coding for phylogenetic reconstruction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Palaeotemperature trend for Precambrian life inferred from resurrected proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

A Bayesian framework for the analysis of cospeciation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Estimating species trees from unrooted gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

A Bayesian model for detecting past recombination events in DNA multiple alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Bayesian sampling of genomic rearrangement scenarios via double cut and join

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Bayesian estimation of the number of inversions in the history of two chromosomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

A simple algorithm to infer gene duplication and speciation events on a gene tree.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU048

Inferring optimal species trees under gene duplication and loss

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Simultaneous identification of duplications and lateral gene transfers.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Gene tree distributions under the coalescent process

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

Vertebrate phylogenomics: reconciled trees and gene duplications.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4265139

27 October 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25070970

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/SYSBIO/SYU048

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25070970%20AND%20SRC:MED&resulttype=core&format=json