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Name | Description | Since | |||
MCMC_SEQ | Co-estimation of reticulate phylogenies and gene trees on sequences from multiple independent loci. | 3.6.1 | |||
Simulates gene trees under a phylogenetic network model. | 3.6.1 | ||||
Uses Gibbs Sampling to explore the hypothesis of the evolutionary history from a collection of gene trees. | 3.6.0 | ||||
MCMC_GT | Bayesian estimation of the posterior distribution of phylogenetic networks (ILS & hybridization) given a list of gene tree topologies. | 3.6.0 | |||
CalIntroRate | Quantifies the introgression probability for each reticulation branch in a given phylogenetic network. | 3.6.0 | |||
InferNetwork_MPL | Infers the species network (ILS & hybridization) from gene trees using maximum pseudo-likelihood. | 3.5.5 | |||
HmmCommand | Uses a hidden markov to assign a species tree to each loci in data coming from a species network. | 3.5.4 | |||
InferNetwork_ML_Bootstrap | Infers the species network (ILS & hybridization) from gene trees using maximum likelihood with parametric bootstrap. | 3.5.2 | |||
InferNetwork_ML_CV | Infers the species network (ILS & hybridization) from gene trees using maximum likelihood with cross-validation. | 3.5.2 | |||
InferNetwork_ML | Infers the species network (ILS & hybridization) from gene trees using maximum likelihood. | 3.4.0 | |||
InferNetwork_MP | Infers the species network (ILS & hybridization) from gene trees under MDC criterion using parsimony-based method. | 3.4.0 | |||
DeepCoalCount_network | Counts the number of extra lineages contributed by a species network and a set of gene trees. | 3.3.0 | |||
Computes the likelihood of a phylogenetic network given a collection of gene trees. | 3.3.0 | ||||
Computes the trees, tripartitions and clusters contained in a phylogenetic network. | 3.0.0 | ||||
Computes the distance between two phylogenetic networks based on their topologies. | 3.0.0 | ||||
Computes the number of coalescent scenarios that can explain the incongruence observed between two trees. | 3.0.0 | ||||
Counts the number of extra lineages contributed by a species tree and a set of gene trees. | 3.0.0 | ||||
Generates CPLEX input for a species tree and a set of gene trees. | 3.0.0 | ||||
Generates species tree topologies based on maximal sets of compatible clusters. | 3.0.0 | ||||
Infers the species tree using bootstrap with existing | 3.0.0 | ||||
Infers the species tree from gene trees using Democratic Vote. | 3.0.0 | ||||
Infers the species tree by GLASS. | 3.0.0 | ||||
Infers the species tree from gene trees using greedy consensus which can deal with gene trees having multiple alleles in species and unrooted gene trees. | 3.0.0 | ||||
Infers the species tree using the “Minimize Deep Coalescence” (MDC) criterion. | 3.0.0 | ||||
Infers the species tree using MDC criterion but also considering time. | 3.0.0 | ||||
Infers the species tree from unrooted gene trees using MDC criterion. | 3.0.0 | ||||
Computes the least common ancestor of a group of nodes in a tree. | 3.0.0 | ||||
Computes a Maximum Agreement Subtree of a pair of trees. | 3.0.0 | ||||
Refines and roots gene trees with respect to a rooted binary species tree under MDC criterion. | 3.0.0 | ||||
Detects and reconstructs horizontal gene transfer events from phylogenetic incongruence. | 3.0.0 | Simulates gene trees under the phylogenetic network model. | 3.0.0 | ||
Computes the symmetric difference, also known as the Robinson-Foulds (RF) distance, between two trees. | 3.0.0 |