Solver¶
CassiopeiaSolvers¶
We have several algorithms available for solving phylogenies:
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The Hybrid Cassiopeia solver. |
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The Cassiopeia ILP-based maximum parsimony solver. |
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A MaxCut graph-based CassiopeiaSolver. |
A CassioepiaGreedy solver with the max cut criterion. |
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Neighbor-Joining class for Cassiopeia. |
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A top-down percolatin-based CassiopeiaSolver. |
Shared-Mutation-Joining class for Cassiopeia. |
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A spectral-based CassiopeiaSolver. |
A CassiopeiaGreedy solver with a spectral heuristic. |
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UPGMA CassiopeiaSolver. |
A class for the basic Cassiopeia-Greedy solver. |
Dissimilarity Maps¶
For use in our distance-based solver and for comparing character states, we also have available several dissimilarity functions:
Compute the dissimilarity between (possibly) ambiguous character strings. |
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Computes the vanilla hamming distance between two samples. |
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A function to return the number of (non-missing) character/state mutations shared by two samples, normalized over the amount of missing data. |
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A function to return the number of (non-missing) character/state mutations shared by two samples. |
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Computes the weighted hamming distance between samples. |
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A function to return the weighted number of (non-missing) character/state mutations shared by two samples. |