pylogeny.pll module
Wrap C extension for libpll library for use in natural Python.
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class pylogeny.pll.dataModel(topo, alignm, model=None)[source]
Encapsulating a phylogenetic tree (as topology) + corresponding alignment
into a libpll-associated data structure. Allows for log-likelihood
scoring of this model. MUST BE CLOSED AFTER USE.
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__init__(topo, alignm, model=None)[source]
Initialize the data model and respective structures.
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close()[source]
If done with this particular problem. Frees associated memory.
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getLogLikelihood()[source]
Calculates log-likelihood using libpll.
| Returns: | a floating point value |
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getNewickString()[source]
Acquire the Newick string of the problem instance.
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class pylogeny.pll.partitionModel(ali)[source]
A partition model intended for libpll.
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__init__(ali)[source]
Initialize a partition model (for internal use by libpll).
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close()[source]
Delete file.
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createModel(models, partnames, ranges)[source]
Establish a more complex model.
| Parameters: |
- models (a list of strings) – a list of model names (e.g., ‘WAG’, ‘DNA’)
- partnames (a list of strings) – a list of partition names (e.g., ‘p1’, ‘p2’)
- ranges (a list of integer tuples) – a list of range tuples (what ranges of alignment)
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| Returns: | None
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createSimpleModel(pmodel='WAG')[source]
Establish a simple model (e.g., one type).
| Parameters: | pmodel (a string (default ‘WAG’)) – optional; what protein model to use (as described in pll) |
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| Returns: | None |
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getFileName()[source]
Get the file name of the model file.