pylogeny.heuristic module
Define the interface for a heuristic in order to implement any manner of heuristic
for a combinatorial problem that can be abstracted into a state graph. In this case, a
phylogenetic tree space.
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class pylogeny.heuristic.RAxMLIdentify(ls, startNode, workdir='.rxml')[source]
Bases: pylogeny.heuristic.phylogeneticLinearHeuristic
RAxML-driven landscape evaluation
of intermediate checkpoint trees output from the
RAxML executable.
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__init__(ls, startNode, workdir='.rxml')[source]
Initialize this heuristic.
| Parameters: |
- ls (a landscape.landscape object) – a landscape object
- startNode (a node (dictionary) from the landscape (getNode())) – what node to start with
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explore()[source]
Explore using RAxML.
| Returns: | None; landscape is modified. |
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class pylogeny.heuristic.heuristic(G=None, start=None)[source]
Bases: object
A base interface for a heuristic that explores a state graph.
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__init__(G=None, start=None)[source]
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explore()[source]
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getStartState()[source]
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getStateGraph()[source]
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class pylogeny.heuristic.likelihoodGreedy(ls, startNode)[source]
Bases: pylogeny.heuristic.phylogeneticLinearHeuristic
Greedy (hill-climbing) landscape exploration by comparsion of
likelihood.
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__init__(ls, startNode)[source]
Initialize this heuristic.
| Parameters: |
- ls (a landscape.landscape object) – a landscape object
- startNode (a node (dictionary) from the landscape (getNode())) – what node to start with
|
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explore()[source]
Perform greedy search of the landscape using
a method of greed via likelihood.
| Returns: | None; landscape is modified |
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class pylogeny.heuristic.parsimonyGreedy(ls, startNode)[source]
Bases: pylogeny.heuristic.phylogeneticLinearHeuristic
Greedy (hill-climbing) landscape exploration by comparsion of parsimony.
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__init__(ls, startNode)[source]
Initialize this heuristic.
| Parameters: |
- ls (a landscape.landscape object) – a landscape object
- startNode (a node (dictionary) from the landscape (getNode())) – what node to start with
|
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explore()[source]
Perform greedy search of the landscape using
a method of greed via parsimonious criterion.
| Returns: | None; landscape is modified |
|---|
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class pylogeny.heuristic.phylogeneticLinearHeuristic(ls, startNode)[source]
Bases: pylogeny.heuristic.heuristic
A base class for a heuristic that works on a phylogenetic landscape
and only possesses a single path (of search).
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__init__(ls, startNode)[source]
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bestTree = None
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getBestTree()[source]
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getPath()[source]
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path = []
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class pylogeny.heuristic.smoothGreedy(ls, startNode)[source]
Bases: pylogeny.heuristic.phylogeneticLinearHeuristic
Parsimony-driven greedy landscape exploration
by comparsion of likelihoods.
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__init__(ls, startNode)[source]
Initialize this heuristic.
| Parameters: |
- ls (a landscape.landscape object) – a landscape object
- startNode (a node (dictionary) from the landscape (getNode())) – what node to start with
|
|---|
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explore()[source]
Perform greedy search of the landscape using
a method of greed via parsimonious criterion and then
performing final smoothing via likelihood on top 10% of
1-SPR neighbors ranked on basis of parsimony.
| Returns: | None; landscape is modified |
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