PoMo: An Allele Frequency-Based Approach for Species Tree Estimation (Q36159728)

12 August 2017

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation (English)

1 reference

12 August 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Dominik Schrempf

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

author name string

Carolin Kosiol

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

publication date

23 July 2015

1 reference

12 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

volume

64

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14 June 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

page(s)

1018-1031

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

14 June 2020

cites work

1 reference

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2 October 2017

1 reference

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Great ape genetic diversity and population history

2 October 2017

1 reference

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Genome-scale coestimation of species and gene trees.

2 October 2017

1 reference

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Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy

2 October 2017

1 reference

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

2 October 2017

1 reference

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Bayesian phylogenetics with BEAUti and the BEAST 1.7

2 October 2017

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

2 October 2017

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Is recombination a problem for species-tree analyses?

2 October 2017

1 reference

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PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals

2 October 2017

1 reference

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phangorn: phylogenetic analysis in R

2 October 2017

1 reference

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

2 October 2017

1 reference

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Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

2 October 2017

1 reference

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Reconstructing population histories from single nucleotide polymorphism data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Composite likelihood-based inferences on genetic data from dependent loci

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Bayesian inference of species trees from multilocus data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Ancestral population genomics: the coalescent hidden Markov model approach

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Coalescent methods for estimating phylogenetic trees

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Gene tree discordance, phylogenetic inference and the multispecies coalescent

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Is a new and general theory of molecular systematics emerging?

2 October 2017

1 reference

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A two-stage pruning algorithm for likelihood computation for a population tree

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Estimating species trees using multiple-allele DNA sequence data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Inconsistency of phylogenetic estimates from concatenated data under coalescence

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Whole-genome re-sequencing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Discordance of species trees with their most likely gene trees.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Inferring phylogeny despite incomplete lineage sorting

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

HyPhy: hypothesis testing using phylogenies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

2 October 2017

1 reference

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A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates

2 October 2017

1 reference

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Evolutionary trees from DNA sequences: A maximum likelihood approach

2 October 2017

1 reference

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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

2 October 2017

1 reference

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The neighbor-joining method: a new method for reconstructing phylogenetic trees

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Relationships between gene trees and species trees

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Estimating species trees using approximate Bayesian computation.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Estimating species phylogenies using coalescence times among sequences.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Incomplete lineage sorting: consistent phylogeny estimation from multiple loci.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

Consistency of estimators of population scaled parameters using composite likelihood.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604832

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

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV048

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYV048

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

PubMed publication ID

26209413

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26209413%20AND%20SRC:MED&resulttype=core&format=json