PhyloNet 3.X.X Commands
Computes the trees, tripartitions and clusters contained in a phylogenetic network. |
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Computes the distance between two phylogenetic networks based on their topologies. |
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Computes the number of coalescent scenarios that can explain the incongruence observed between two trees. |
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Count the number of extra lineages contributed by a species tree and a set of gene trees. |
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Generates CPLEX input for a species tree and a set of gene trees. |
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Generates species tree topologies based on maximal sets of compatible clusters. |
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Infers the species tree using bootstrap with existing |
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Infer the species tree from gene trees using Democratic Vote. |
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Infer the species tree by GLASS. |
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Infer the species tree from gene trees using an extended version of Majority Consensus which can deal with gene trees having multiple alleles in species and unrooted gene trees. |
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Infer the species tree using the “Minimize Deep Coalescence” (MDC) criterion. |
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Infer the species tree using MDC criterion but also considering time. |
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Computes the least common ancestor of a group of nodes in a tree. |
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Computes a Maximum Agreement Subtree of a pair of trees. |
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Refine and root gene trees with respect to a rooted binary species tree under MDC criterion. |
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Detects and reconstructs horizontal gene transfer events from phylogenetic incongruence. |
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Computes the symmetric difference, also known as the Robinson-Foulds (RF) distance, between two trees. |