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A stochastic simulator of birth-death master equations with application to phylodynamics.

Vaughan TG, Drummond AJ - Mol. Biol. Evol. (2013)

Bottom Line: Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics.Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes.Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

View Article: PubMed Central - PubMed

Affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. t.g.vaughan@massey.ac.nz

ABSTRACT
In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

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Relationship between populations and population types in MASTER.
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mst057-F8: Relationship between populations and population types in MASTER.

Mentions: MASTER achieves this goal by grouping all populations within the scope of the model into one or more population types. The populations within each type are arranged into a -dimensional array where is a vector of positive integers specifying the size of the array in each dimension. The general effect of this is that both a type name and a cell location within the corresponding array are necessary to specify a particular population in a MASTER model. The relationship between populations and population types is illustrated in figure 8.Fig. 8.


A stochastic simulator of birth-death master equations with application to phylodynamics.

Vaughan TG, Drummond AJ - Mol. Biol. Evol. (2013)

Relationship between populations and population types in MASTER.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3649681&req=5

mst057-F8: Relationship between populations and population types in MASTER.
Mentions: MASTER achieves this goal by grouping all populations within the scope of the model into one or more population types. The populations within each type are arranged into a -dimensional array where is a vector of positive integers specifying the size of the array in each dimension. The general effect of this is that both a type name and a cell location within the corresponding array are necessary to specify a particular population in a MASTER model. The relationship between populations and population types is illustrated in figure 8.Fig. 8.

Bottom Line: Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics.Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes.Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

View Article: PubMed Central - PubMed

Affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. t.g.vaughan@massey.ac.nz

ABSTRACT
In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

Show MeSH