Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses (Q35667118)

9 August 2017

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses (English)

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9 August 2017

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9 August 2017

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9 August 2017

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Tandy Warnow

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9 August 2017

Md Shamsuzzoha Bayzid

series ordinal

1

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PubMed ID

26086579

9 August 2017

language of work or name

English

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publication date

18 June 2015

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9 August 2017

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9 August 2017

e0129183

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Creative Commons Attribution 4.0 International

9 August 2017

start time

18 June 2015

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

1 reference

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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

12 July 2018

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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

12 July 2018

1 reference

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Whole-genome analyses resolve early branches in the tree of life of modern birds

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Phylotranscriptomic analysis of the origin and early diversification of land plants

12 July 2018

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ASTRAL: genome-scale coalescent-based species tree estimation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Quartet inference from SNP data under the coalescent model

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Discordance of species trees with their most likely gene trees: a unifying principle.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Identifying localized biases in large datasets: a case study using the avian tree of life

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Is recombination a problem for species-tree analyses?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Properties of consensus methods for inferring species trees from gene trees

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

DendroPy: a Python library for phylogenetic computing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Bayesian inference of species trees from multilocus data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Fast and consistent estimation of species trees using supermatrix rooted triples

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

INDELible: a flexible simulator of biological sequence evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Gene tree discordance, phylogenetic inference and the multispecies coalescent

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Is a new and general theory of molecular systematics emerging?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Inconsistency of phylogenetic estimates from concatenated data under coalescence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Joint Bayesian Estimation of Alignment and Phylogeny

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

MRBAYES: Bayesian inference of phylogenetic trees

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

The general stochastic model of nucleotide substitution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Inferring ancient divergences requires genes with strong phylogenetic signals.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Estimating species trees from unrooted gene trees.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Estimating species phylogenies using coalescence times among sequences.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4472720

Error in Phylogenetic Estimation for Bushes in the Tree of Life

25 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0129183

New methods to color the vertices of a graph

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0129183

On Information and Sufficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0129183

PASTA: Ultra-Large Multiple Sequence Alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0129183

Naive binning improves phylogenomic analyses

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26086579

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0129183

1 reference

9 August 2017

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9 August 2017

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PubMed ID

26086579