(Q35134254)

24678701

6 August 2017

title

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines (English)

1 reference

6 August 2017

1 reference

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Noah Rosenberg

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

4

Aaron Liston

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

6

David B Neale

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

author name string

Michael DeGiorgio

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

John Syring

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Andrew J Eckert

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

publication date

29 March 2014

1 reference

24678701

6 August 2017

published in

BMC Evolutionary Biology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

volume

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

page(s)

67

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1186/1471-2148-14-67

12 June 2020

exact match

0 references

cites work

State-of the art methodologies dictate new standards for phylogenetic analysis

1 reference

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

28 July 2018

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

28 July 2018

1 reference

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Improvements to a class of distance matrix methods for inferring species trees from gene trees.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

iGLASS: an improvement to the GLASS method for estimating species trees from gene trees.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Fast and accurate methods for phylogenomic analyses

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

An experimental study of Quartets MaxCut and other supertree methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

What is the danger of the anomaly zone for empirical phylogenetics?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Bayesian inference of species trees from multilocus data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Fast and consistent estimation of species trees using supermatrix rooted triples

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

PineSAP--sequence alignment and SNP identification pipeline

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Coalescent methods for estimating phylogenetic trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus arntzenii) (corrected)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Rooted triple consensus and anomalous gene trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

High-resolution species trees without concatenation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Inconsistency of phylogenetic estimates from concatenated data under coalescence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

The supermatrix approach to systematics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Discordance of species trees with their most likely gene trees.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

MUSCLE: multiple sequence alignment with high accuracy and high throughput

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Base-calling of automated sequencer traces using phred. II. Error probabilities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Robustness to divergence time underestimation when inferring species trees from estimated gene trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Mathematical properties of the deep coalescence cost.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Inferring ancient divergences requires genes with strong phylogenetic signals.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Estimating species trees from unrooted gene trees.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Consistency properties of species tree inference by minimizing deep coalescences.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

The accuracy of species tree estimation under simulation: a comparison of methods

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Species trees from highly incongruent gene trees in rice.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Estimating species phylogenies using coalescence times among sequences.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Properties of consensus methods for inferring species trees from gene trees

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Incomplete lineage sorting: consistent phylogeny estimation from multiple loci.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Species tree inference by minimizing deep coalescences

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Gene tree discordance, phylogenetic inference and the multispecies coalescent

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Maximum tree: a consistent estimator of the species tree.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Reticulate evolution and incomplete lineage sorting among the ponderosa pines

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

BEST: Bayesian estimation of species trees under the coalescent model.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Phylogenetic inference using whole genomes

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Estimating species trees using multiple-allele DNA sequence data

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Genomic diversity in forest trees

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Bayesian estimation of concordance among gene trees.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Genome-scale approaches to resolving incongruence in molecular phylogenies

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4021425

Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci

16 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24678701

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Confidence Limits on Phylogenies: an Approach using the Bootstrap

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24678701

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SEARCHING FOR EVOLUTIONARY PATTERNS IN THE SHAPE OF A PHYLOGENETIC TREE.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24678701

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2148-14-67

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

12 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

24678701

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24678701%20AND%20SRC:MED&resulttype=core&format=json