(Q29617331)

English

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

6 July 2017

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified (English)

1 reference

Europe PubMed Central

6 July 2017

Christopher J. Creevey

2

1 reference

Europe PubMed Central

6 July 2017

Thomas M. Keane

object named as

Thomas M Keane

1

0 references

author name string

Melissa M Pentony

3

1 reference

Europe PubMed Central

6 July 2017

Thomas J Naughton

4

1 reference

Europe PubMed Central

6 July 2017

James O Mclnerney

5

1 reference

Europe PubMed Central

6 July 2017

language of work or name

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=16563161

30 April 2017

publication date

24 March 2006

1 reference

Europe PubMed Central

6 July 2017

BMC Evolutionary Biology

1 reference

Europe PubMed Central

6 July 2017

6

1 reference

Europe PubMed Central

6 July 2017

1

0 references

29

1 reference

Europe PubMed Central

6 July 2017

https://scigraph.springernature.com/pub.10.1186/1471-2148-6-29

0 references

ProtTest: selection of best-fit models of protein evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Different versions of the Dayhoff rate matrix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Phylogenomics of eukaryotes: impact of missing data on large alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

PAML: a program package for phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Evolutionary trees from DNA sequences: A maximum likelihood approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

The rapid generation of mutation data matrices from protein sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

Amino acid substitution matrices from protein blocks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

30 April 2017

The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Modeling compositional heterogeneity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Clann: investigating phylogenetic information through supertree analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Chloroplast phylogeny indicates that bryophytes are monophyletic

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Model misspecification and probabilistic tests of topology: evidence from empirical data sets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

HOVERGEN: a database of homologous vertebrate genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Success of maximum likelihood phylogeny inference in the four-taxon case

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

3 June 2018

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Accounting for Uncertainty in the Tree Topology Has Little Effect on the Decision-Theoretic Approach to Model Selection in Phylogeny Estimation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

A transition probability model for amino acid substitutions from blocks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Selecting the best-fit model of nucleotide substitution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Topological bias and inconsistency of maximum likelihood using wrong models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Models of amino acid substitution and applications to mitochondrial protein evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435933

26 November 2018

Model of amino acid substitution in proteins encoded by mitochondrial DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/16563161

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The effect of topology on estimates of among-site rate variation

1 reference

https://pubmed.ncbi.nlm.nih.gov/16563161

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation

1 reference

https://pubmed.ncbi.nlm.nih.gov/16563161

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?

1 reference

https://pubmed.ncbi.nlm.nih.gov/16563161

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modeling amino acid replacement

1 reference

https://pubmed.ncbi.nlm.nih.gov/16563161

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method

1 reference

https://pubmed.ncbi.nlm.nih.gov/16563161

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2148-6-29

1 reference

Europe PubMed Central

6 July 2017

Dimensions Publication ID

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-6-29

9 September 2019

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Europe PubMed Central

6 July 2017

1 reference

Europe PubMed Central

6 July 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q29617331&oldid=1990234666"