PhyloNet 3.X.X Commands
Name | Description | Since |
| ExploreHypothesis_GibbsSampling | 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 the 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 |