DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference
نویسندگان
چکیده
منابع مشابه
Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured b...
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Genomics is increasingly being used to investigate disease outbreaks, but an important question remains unanswered--how well do genomic data capture known transmission events, particularly for pathogens with long carriage periods or large within-host population sizes? Here we present a novel Bayesian approach to reconstruct densely sampled outbreaks from genomic data while considering within-ho...
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The combination of a Markov chain Monte Carlo (MCMC) method with likelihood-based assessment of phylogenies is becoming a popular alternative to direct likelihood optimization. However, MCMC, like maximum likelihood, is a computationally expensive method. To approximate the posterior distribution of phylogenies, a Markov chain is constructed, using the Metropolis algorithm, such that the chain ...
متن کاملPolytomies and Bayesian phylogenetic inference.
Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of...
متن کاملRelating phylogenetic trees to transmission trees of infectious disease outbreaks.
Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pa...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2018
ISSN: 1471-2105
DOI: 10.1186/s12859-018-2347-3