Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method (Q34977974)

5 August 2017

title

Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method (English)

1 reference

5 August 2017

6

Qifa Zhang

1 reference

5 August 2017

Chengjun Zhang

1

1 reference

5 August 2017

Jia Wang

2

1 reference

5 August 2017

Weibo Xie

3

1 reference

5 August 2017

Gang Zhou

4

1 reference

5 August 2017

Manyuan Long

5

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5 August 2017

language of work or name

English

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publication date

26 April 2011

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Proceedings of the National Academy of Sciences of the United States of America

5 August 2017

published in

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5 August 2017

volume

108

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5 August 2017

issue

19

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5 August 2017

page(s)

7860-7865

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Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae).

5 August 2017

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Distinct evolutionary patterns between two duplicated color vision genes within cyprinid fishes

8 July 2018

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In defense of statistical methods for detecting positive selection

8 July 2018

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Divergence in function and expression of the NOD26-like intrinsic proteins in plants

8 July 2018

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The evolution of color vision in nocturnal mammals

8 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=3093512

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Molecular evolution of the betagamma lens crystallin superfamily: evidence for a retained ancestral function in gamma N crystallins?

8 July 2018

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Recent origins of sperm genes in Drosophila

8 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=3093512

Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae).

8 July 2018

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Adaptive functional divergence among triplicated alpha-globin genes in rodents

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Evidence for positive selection in the C-terminal domain of the cholesterol metabolism gene PCSK9 based on phylogenetic analysis in 14 primate species

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Molecular evolution of the human SRPX2 gene that causes brain disorders of the Rolandic and Sylvian speech areas

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

PAML 4: phylogenetic analysis by maximum likelihood

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Duplication and divergence of 2 distinct pancreatic ribonuclease genes in leaf-eating African and Asian colobine monkeys

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Parallel evolution of chimeric fusion genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Inference of selection from multiple species alignments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Statistical tests of models of DNA substitution.

8 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea).

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Gene conversion and functional divergence in the beta-globin gene family

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Lineage-specific duplication and loss of pepsinogen genes in hominoid evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Divergence of recently duplicated M{gamma}-type MADS-box genes in Petunia

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Pistillata--duplications as a mode for floral diversification in (Basal) asterids

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Adaptive evolution and frequent gene conversion in the brain expressed X-linked gene family in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Molecular evolution of PISTILLATA-like genes in the dogwood genus Cornus (Cornaceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Purifying selection is a prevailing motif in the evolution of ketoacyl synthase domains of polyketide synthases from lichenized fungi

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Inactivation of MOXD2 and S100A15A by exon deletion during human evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Rapid evolution, genetic variations, and functional association of the human spermatogenesis-related gene NYD-SP12.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

A new look at the statistical model identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018621108

Evidence for positive Darwinian selection on the hepcidin gene of Perciform and Pleuronectiform fishes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Adaptive evolution after duplication of penaeidin antimicrobial peptides

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093512

Purifying selection and positive selection on the myxovirus resistance gene in mammals and chickens

26 October 2018

1 reference

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Adaptive evolution of 5'HoxD genes in the origin and diversification of the cetacean flipper

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Adaptive evolution of rbcL in Conocephalum (Hepaticae, bryophytes)

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Adaptive evolution of digestive RNASE1 genes in leaf-eating monkeys revisited: new insights from ten additional colobines

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High molecular diversity in the rhodopsin gene in closely related goby fishes: A role for visual pigments in adaptive speciation?

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The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms

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Identifiers

DOI

10.1073/PNAS.1018621108

1 reference

5 August 2017

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1 reference

5 August 2017

1 reference