(Q34701661)

4 August 2017

title

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices (English)

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4 August 2017

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3

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4 August 2017

Jenna Morgan Lang

1

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Aaron Earl Darling

object named as

Aaron E Darling

series ordinal

2

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language of work or name

English

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publication date

25 April 2013

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4 August 2017

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4 August 2017

volume

8

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4 August 2017

issue

4

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4 August 2017

page(s)

e62510

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Creative Commons CC0 License

4 August 2017

copyright license

start time

25 April 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

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cites work

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7 July 2018

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

7 July 2018

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Phylogenetic inference via sequential Monte Carlo

7 July 2018

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IMG: the Integrated Microbial Genomes database and comparative analysis system

7 July 2018

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Fast and accurate methods for phylogenomic analyses

7 July 2018

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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

7 July 2018

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An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia

7 July 2018

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The phylogenetic diversity of metagenomes

7 July 2018

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Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2))

7 July 2018

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Phylogenomics-based reconstruction of protozoan species tree

7 July 2018

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Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany

7 July 2018

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Telling the whole story in a 10,000-genome world

7 July 2018

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Phylogeny and evolution of the Archaea: one hundred genomes later

7 July 2018

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Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function.

7 July 2018

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Let them fall where they may: congruence analysis in massive phylogenetically messy data sets

7 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=3636077

ProtTest 3: fast selection of best-fit models of protein evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Complete genome sequences of two hemotropic mycoplasmas, Mycoplasma haemofelis strain Ohio2 and Mycoplasma suis Strain Illinois

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

The origin of the Haitian cholera outbreak strain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Phylogeny of gammaproteobacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

A new generation of homology search tools based on probabilistic inference

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Search for a 'Tree of Life' in the thicket of the phylogenetic forest

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

FastTree: computing large minimum evolution trees with profiles instead of a distance matrix

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Infernal 1.0: inference of RNA alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

A rapid bootstrap algorithm for the RAxML Web servers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

A simple, fast, and accurate method of phylogenomic inference

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Uncovering rate variation of lateral gene transfer during bacterial genome evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Estimating species trees using multiple-allele DNA sequence data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Dendroscope: An interactive viewer for large phylogenetic trees

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Insights into the genome of large sulfur bacteria revealed by analysis of single filaments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Cospeciation in the triplex symbiosis of termite gut protists (Pseudotrichonympha spp.), their hosts, and their bacterial endosymbionts.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

The supermatrix approach to systematics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

UniFrac: a new phylogenetic method for comparing microbial communities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Phylogenetic diversity and the greedy algorithm.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Do orthologous gene phylogenies really support tree-thinking?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Assessment of the accuracy of matrix representation with parsimony analysis supertree construction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Phylogenetic analysis of vertically transmitted psyllid endosymbionts (Candidatus Carsonella ruddii) based on atpAGD and rpoC: comparisons with 16S-23S rDNA-derived phylogeny

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Phylogenetic analysis using PHYLIP.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Hippea maritima gen. nov., sp. nov., a new genus of thermophilic, sulfur-reducing bacterium from submarine hot vents

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Speciation durations and Pleistocene effects on vertebrate phylogeography

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Horizontal transfer of ATPase genes--the tree of life becomes a net of life

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Construction of phylogenetic trees

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Basic local alignment search tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Independent origins and horizontal transfer of bacterial symbionts of aphids

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

A likelihood look at the supermatrix-supertree controversy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

Imputing supertrees and supernetworks from quartets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

A review of long-branch attraction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062510

Total evidence, average consensus and matrix representation with parsimony: what a difference distances make.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Bacterial molecular phylogeny using supertree approach.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636077

Matrix representation with parsimony, taxonomic congruence, and total evidence

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23638103

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0062510

1 reference

4 August 2017

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1 reference

4 August 2017

1 reference