Incorporating indel information into phylogeny estimation for rapidly emerging pathogens (Q33278628)

25 July 2017

title

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens (English)

1 reference

25 July 2017

1 reference

1 reference

Marc A Suchard

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25 July 2017

Benjamin D Redelings

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25 July 2017

publication date

14 March 2007

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25 July 2017

published in

BMC Evolutionary Biology

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25 July 2017

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25 July 2017

1 reference

Incorporating information from length-mutational events into phylogenetic analysis.

25 July 2017

cites work

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Joint Bayesian Estimation of Alignment and Phylogeny

21 June 2018

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Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.

21 June 2018

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Phylogenetic analysis of polyomavirus simian virus 40 from monkeys and humans reveals genetic variation

21 June 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

The causes and consequences of HIV evolution

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Iterative pass optimization of sequence data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Molecular evolution of insertions and deletion in the chloroplast genome of silene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Gaps as characters in sequence-based phylogenetic analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Rare genomic changes as a tool for phylogenetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Reassortment and insertion-deletion are strategies for the evolution of influenza B viruses in nature

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

In vivo dynamics of equine infectious anemia viruses emerging during febrile episodes: insertions/duplications at the principal neutralizing domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Evolution of a noncoding region of the chloroplast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Alignment-ambiguous nucleotide sites and the exclusion of systematic data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

A codon-based model of nucleotide substitution for protein-coding DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

The order of sequence alignment can bias the selection of tree topology.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

An evolutionary model for maximum likelihood alignment of DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Evidence that eukaryotes and eocyte prokaryotes are immediate relatives

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Inching toward reality: an improved likelihood model of sequence evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Indel patterns of the plastid DNA trnL- trnF region within the genus Poa (Poaceae).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

A novel use of equilibrium frequencies in models of sequence evolution

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Long-term follow-up study of core gene deletion mutants in children with chronic hepatitis B virus infection.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1853084

Antigenic stimulation by BCG vaccine as an in vivo driving force for SIV replication and dissemination

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17359539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The evolution of the atpbeta-rbcL intergenic spacer in the epacrids (Ericales) and its systematic and evolutionary implications

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17359539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Freeing phylogenies from artifacts of alignment

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17359539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2148-7-40

1 reference

Dimensions Publication ID

25 July 2017

0 references

1 reference

25 July 2017

1 reference