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Class Summary |
| Bootstrap |
This class use bootstrap to infer species tree |
| ClusteringInference |
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| CoalescentCounter |
This class counts the number of coalescents supported by two trees. |
| CoalescentCounterTestCase |
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| DeepCoalescencesCounter |
This class counts the number of deep coalescences for a species tree given a set of gene trees. |
| DemocraticVoteInference |
This class uses democratic vote to infer the species tree from gene trees |
| GeneTreeRefinement |
This class refines and roots gene trees with respect to a given rooted binary species tree
"Algorithms for MDC-based multi-locus phylogeny inference." RECOMB 2011 |
| GLASSInference |
This class uses GLASS to infer the species tree from gene trees. |
| MajorityConsensusInference |
This class use extended Majority Consensus to infer the species tree from gene trees |
| MDCInference_DP |
Class for inferring the species tree from a set of rooted gene trees by minimizing deep coalescence number. |
| MDCInference_ILP |
This class is for inferring the species tree from gene trees, by minimizing the number of coalescences. |
| MDCURInference |
Class for inferring the species tree from a set of unrooted gene trees by minimizing deep coalescence number. |
| MDCURInference_DP |
Class for inferring the species tree from a set of unrooted gene trees by minimizing deep coalescence number. |
| MDCURInference_ILP |
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| MDCWithTime |
Class for inferring the species tree from a set of unrooted gene trees by minimizing deep coalescence number. |
| Solution |
This class saves the result of multiple versions of MDC |
| TaxaDistanceMatrix |
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