(Q34407795)

2 August 2017

A Bayesian approach for fast and accurate gene tree reconstruction (English)

1 reference

2 August 2017

2

Manolis Kellis

1 reference

2 August 2017

Matthew D Rasmussen

1

1 reference

2 August 2017

25 July 2010

1 reference

Molecular Biology and Evolution

2 August 2017

1 reference

2 August 2017

28

1 reference

2 August 2017

1

1 reference

2 August 2017

273-290

1 reference

FastTree 2--approximately maximum-likelihood trees for large alignments

2 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Ancestral population genomics: the coalescent hidden Markov model 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=3002250

Evolution of pathogenicity and sexual reproduction in eight Candida 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=3002250

Berkeley PHOG: PhyloFacts orthology group prediction 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=3002250

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=3002250

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=3002250

Gene family evolution across 12 Drosophila 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=3002250

Evolution of genes and genomes on 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=3002250

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=3002250

Natural history and evolutionary principles of gene duplication in 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=3002250

Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome 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=3002250

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

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=3002250

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=3002250

A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Toward Automatic Reconstruction of a Highly Resolved 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=3002250

Inferring phylogeny despite 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=3002250

TreeFam: a curated database of phylogenetic trees of animal gene families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Estimating the tempo and mode of gene family evolution from comparative genomic 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=3002250

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element 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=3002250

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=3002250

Clann: investigating phylogenetic information through supertree analyses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Genome evolution in yeasts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

The diploid genome sequence of Candida albicans

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae 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=3002250

Gene conversion and the evolution of protocadherin gene cluster diversity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Genome-scale approaches to resolving incongruence in molecular 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=3002250

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=3002250

OrthoMCL: Identification of Ortholog Groups for Eukaryotic 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=3002250

Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

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=3002250

MrBayes 3: Bayesian phylogenetic inference under mixed 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=3002250

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Sequencing and comparison of yeast species to identify genes and regulatory elements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

The genome sequence of Drosophila melanogaster

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary 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=3002250

BIONJ: an improved version of the NJ algorithm based on a simple model of 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=3002250

Molecular evidence for an ancient duplication of the entire yeast 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=3002250

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree 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=3002250

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=3002250

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

The neighbor-joining method: a new method for reconstructing 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=3002250

Basic local alignment search tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3002250

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

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

NOTUNG: a program for dating gene duplications and optimizing gene family trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

Space of gene/species trees reconciliations and parsimonious models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

A hybrid micro-macroevolutionary approach to gene tree reconstruction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

My worries are no longer behind me.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

Maps between Trees and Cladistic Analysis of Historical Associations Among Genes, Organisms, and Areas

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ189

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%2FMOLBEV%2FMSQ189

Very low gene duplication rate in the yeast genome

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20660489

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genome phylogenetic analysis based on extended gene contents

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20660489

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSQ189

1 reference

2 August 2017

1 reference

2 August 2017

1 reference

PubMed ID

20660489