(Q33793566)

29 July 2017

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference (English)

1 reference

29 July 2017

1 reference

2

Hervé Philippe

1 reference

29 July 2017

Béatrice Roure

1

1 reference

29 July 2017

14 January 2011

1 reference

29 July 2017

BMC Evolutionary Biology

1 reference

29 July 2017

11

1 reference

29 July 2017

17

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-11-17

29 July 2017

0 references

cites work

Among-site rate variation and its impact on phylogenetic analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Recovering evolutionary trees under a more realistic model of sequence evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Phylogenomics revives traditional views on deep animal relationships

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Additional molecular support for the new chordate phylogeny

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Broad phylogenomic sampling improves resolution of the animal tree of life

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Acoel flatworms are not platyhelminthes: evidence from phylogenomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Deciphering ancient rapid radiations

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Identifying dramatic selection shifts in phylogenetic trees

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Mitochondrial genome of the homoscleromorph Oscarella carmela (Porifera, Demospongiae) reveals unexpected complexity in the common ancestor of sponges and other animals

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Phylogenomics: the beginning of incongruence?

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Phylogenomics and the reconstruction of the tree of life

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Genome-scale phylogeny and the detection of systematic biases

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Heterotachy, an important process of protein evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Parallel adaptive radiations in two major clades of placental mammals

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Estimation of primate speciation dates using local molecular clocks

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

A compound poisson process for relaxing the molecular clock

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Estimating the rate of evolution of the rate of molecular evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Assessing the impact of secondary structure and solvent accessibility on protein evolution.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Modeling the covarion hypothesis of nucleotide substitution.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

MUST, a computer package of Management Utilities for Sequences and Trees

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

On the use of nucleic acid sequences to infer early branchings in the tree of life

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Evolutionary trees from DNA sequences: A maximum likelihood approach

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

A simple method for displaying the hydropathic character of a protein

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

The nonidentity of invariable positions in the cytochromes c of different species

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3034684

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

4 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Combining protein evolution and secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Mathematical elegance with biochemical realism: the covarion model of molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

On the conservation of protein sequences in evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

An improved statistical method for detecting heterotachy in nucleotide sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Maximum-likelihood phylogenetic analysis under a covarion-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Testing for covarion-like evolution in protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Empirical profile mixture models for phylogenetic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

The root of the tree of life in the light of the covarion model

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

A Bayesian Analysis of Some Nonparametric Problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-17

Testing a covariotide model of DNA substitution

21 January 2018

1 reference

12 December 2020

Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes

1 reference

12 December 2020

Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models

1 reference

12 December 2020

How molecules evolve in eubacteria

1 reference

12 December 2020

Inferences from protein and nucleic acid sequences: early molecular evolution, divergence of kingdoms and rates of change

1 reference

12 December 2020

Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers

1 reference

12 December 2020

Modeling evolution at the protein level using an adjustable amino acid fitness model

1 reference

12 December 2020

Modeling residue usage in aligned protein sequences via maximum likelihood

1 reference

12 December 2020

Model of amino acid substitution in proteins encoded by mitochondrial DNA

1 reference

12 December 2020

Animal evolution and the molecular signature of radiations compressed in time

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-11-17

1 reference

PubMed ID

21235782

Dimensions Publication ID

29 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-11-17

9 September 2019

1 reference

29 July 2017

1 reference

PubMed ID

21235782