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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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Simulating a serially sampled coalescent tree. (a) Inheritance relationships between coalescing individuals. (b) A typical tree generated using the chosen leaf times and coalescence rate. Note the late introduction of lineages at times , extending the age of the root substantially.
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mst057-F6: Simulating a serially sampled coalescent tree. (a) Inheritance relationships between coalescing individuals. (b) A typical tree generated using the chosen leaf times and coalescence rate. Note the late introduction of lineages at times , extending the age of the root substantially.

Mentions: The “:1” following each reactant population identifier causes MASTER to regard those reactants as parents of each of the reaction products which carry the same suffix. We could have used any integer following the colon, as long as the same integer is appended to all products and reactants which are to be regarded as parents/children of one another. This particular reaction specification results in the inheritance relationships shown in figure 6a.Fig. 6.


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

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

Simulating a serially sampled coalescent tree. (a) Inheritance relationships between coalescing individuals. (b) A typical tree generated using the chosen leaf times and coalescence rate. Note the late introduction of lineages at times , extending the age of the root substantially.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

mst057-F6: Simulating a serially sampled coalescent tree. (a) Inheritance relationships between coalescing individuals. (b) A typical tree generated using the chosen leaf times and coalescence rate. Note the late introduction of lineages at times , extending the age of the root substantially.
Mentions: The “:1” following each reactant population identifier causes MASTER to regard those reactants as parents of each of the reaction products which carry the same suffix. We could have used any integer following the colon, as long as the same integer is appended to all products and reactants which are to be regarded as parents/children of one another. This particular reaction specification results in the inheritance relationships shown in figure 6a.Fig. 6.

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