About: Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Incorporating indel information into phylogeny estimation for rapidly emerging pathogens Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
Creator	Redelings, Benjamin Suchard, Marc
source	Medline; PMC
abstract	BACKGROUND: Phylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate in the short times since divergence. To improve resolution of such phylogenies we propose using insertion and deletion (indel) information in addition to substitution information. We accomplish this through joint estimation of alignment and phylogeny in a Bayesian framework, drawing inference using Markov chain Monte Carlo. Joint estimation of alignment and phylogeny sidesteps biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments. RESULTS: We introduce a novel Markov chain transition kernel that improves computational efficiency by proposing non-local topology rearrangements and by block sampling alignment and topology parameters. In addition, we extend our previous indel model to increase biological realism by placing indels preferentially on longer branches. We demonstrate the ability of indel information to increase phylogenetic resolution in examples drawn from within-host viral sequence samples. We also demonstrate the importance of taking alignment uncertainty into account when using such information. Finally, we show that codon-based substitution models can significantly affect alignment quality and phylogenetic inference by unrealistically forcing indels to begin and end between codons. CONCLUSION: These results indicate that indel information can improve phylogenetic resolution of recently diverged pathogens and that alignment uncertainty should be considered in such analyses.
has issue date	2007-03-14(xsd:dateTime)
bibo:doi	10.1186/1471-2148-7-40
bibo:pmid	17359539
has license	cc-by
sha1sum (hex)	4e0851aa892c56090edbc47e9506313d2a1b20e0
schema:url	https://doi.org/10.1186/1471-2148-7-40
resource representing a document's title	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
has PubMed Central identifier	PMC1853084
has PubMed identifier	17359539
schema:publication	BMC Evol Biol
resource representing a document's body	covid:4e0851aa892c56090edbc47e9506313d2a1b20e0#body_text
is schema:about of	named entity 'short' named entity 'Markov chain Monte Carlo' named entity 'phylogeny' named entity 'rapidly' named entity 'phylogenies' named entity 'deletion' named entity 'improve' named entity 'inference' named entity 'phylogeny' named entity 'indel' named entity 'lentivirus' named entity 'viruses' named entity 'pairwise alignment' named entity 'taxa' named entity 'missing data' named entity 'codons' named entity 'indel' named entity 'taxa' named entity 'letter frequencies' named entity 'Severe Acute Respiratory Syndrome' named entity 'gp41' named entity 'indels' named entity 'indels' named entity 'molecular sequences' named entity 'pathogens' named entity 'CTMC' named entity 'codon' named entity 'indels' named entity 'indel' named entity 'variable regions' named entity 'stochastic model' named entity 'China' named entity 'nucleotides' named entity 'positive selection' named entity 'posterior distribution' named entity 'indel' named entity 'indels' named entity 'nucleotides' named entity 'molecular sequence' named entity 'indels' named entity 'Exponential distribution' named entity 'Insertions and deletions' named entity 'gene' named entity 'gp120' named entity 'clades' named entity 'HIV' named entity 'codon' named entity 'indels' named entity 'nucleotide' named entity 'Exponential distribution' named entity 'Hepatitis B virus' named entity 'HBV' named entity 'indel' named entity 'traditional methods' named entity 'MAP' named entity 'indel' named entity 'indels' named entity 'Clustal W' named entity 'indels' named entity 'indels' named entity 'MCMC' named entity 'probability generating function' named entity 'pairwise alignment' named entity 'indel' named entity 'Viral' named entity 'indels' named entity 'transition kernel' named entity 'indels' named entity 'codons' named entity '7.2' named entity 'Muscle' named entity 'posterior distribution' named entity 'gp41' named entity 'collapsing function' named entity '0.9' named entity 'indel' named entity 'MAP' named entity 'nucleotide' named entity 'nucleotide' named entity 'HMM'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2025 OpenLink Software