PhyloNet 3.X.X Commands
("Ref" lists the main reference; clicking on the command takes you to a page that lists all the relevant references.)
Name | Description | Ref | Since | |||
| Methods for Species Network (and Tree) Inference (all account for ILS) | ||||||
| MCMC_SEQ | Co-Bayesian MCMC posterior estimation of reticulate phylogenies phylogenetic networks and gene trees on DNA sequences from multiple independent loci. | here | 3.6.1 | |||
| ExploreHypothesisMCMC_GibbsSamplingBiMarkers | Bayesian estimation of the posterior distribution of phylogenetic networks given bi-allelic genetic markers (SNPs, AFLPs, etc). | hereUses Gibbs Sampling to explore the hypothesis of the evolutionary history from a collection of gene trees. | 3.6. 01 | |||
| MCMC_GT | Bayesian MCMC posterior estimation of the posterior distribution of phylogenetic networks (ILS & hybridization) given a list of gene tree topologies. | here | 3.6.0 | |||
| MLE_BiMarkers | Maximum (pseudo-)likelihood estimation of phylogenetic networks given bi-allelic genetic markers (SNPs, AFLPs, etc). | here | CalIntroRate | Quantifies the introgression probability for each reticulation branch in a given phylogenetic network. | 3.6.04 | |
| InferNetwork_MPL | Infers the species network (ILS & hybridization) a phylogenetic network from gene trees using under maximum pseudo-likelihood. | here | 3.5.5HmmCommand | 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) a phylogenetic network from gene trees using under maximum likelihood with parametric bootstrap. | here | 3.5.2 | ||
| InferNetwork_ML_CV | Infers the species network (ILS & hybridization) a phylogenetic network from gene trees using under maximum likelihood with cross-validation. | here | 3.5.2 | |||
| InferNetwork_ML | Infers the species network (ILS & hybridization) a phylogenetic network from gene trees using under maximum likelihood. | here | 3.4.0 | |||
| InferNetwork_MP | Infers the species network (ILS & hybridization) a phylogenetic network from gene trees under the MDC criterion using parsimony-based method. | here | 3.4.0 | |||
| DeepCoalCountInferNetwork_MP_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 | |||||
| Allopp | Infers an allopolyploid network from gene trees under the MDC criterion. | 3.8.3 | ||||
| NetMerger | Merge subnetworks inferred by MCMC_SEQ or MCMC_BiMarkers to a full network. | here | ||||
| Methods for Species Tree (not Networks) Inference | ||||||
Infers the a species tree using bootstrap with existing | 3.0.0 | |||||
Infers the a species tree from gene trees using the "Democratic Vote" method. | 3.0.0 | |||||
Infers the a species tree by GLASS.using the GLASS method of Mossel and Roch. | here | 3.0.0 | ||||
Infers the a species tree from gene trees using greedy consensus which can deal with (allows for gene trees having with multiple alleles in species and for unrooted gene trees). | 3.0.0 | |||||
Infers the a species tree from gene tree topologies using the “Minimize Deep Coalescence” (MDC) criterion. | here | 3.0.0 | ||||
Infers the a species tree from gene trees with coalescent times using the MDC criterion but also considering time. | 3.0.0 | |||||
Infers the a species tree from unrooted gene trees tree topologies using the MDC criterion. | here | 3.0.0 | ||||
Generates CPLEX input for a species tree and a set of gene trees. | here | 3.0.0 | ||||
Generates species tree topologies based on maximal sets of compatible clusters. | here | 3.0.0 | ||||
Computes the least common ancestor of a group of nodes in a tree. | 3.0.0 | |||||
| Methods for Analyzing Species Trees/Networks with Respect to Locus-specific Data | ||||||
| CalIntroRate | Quantifies the introgression probability for each reticulation branch in a given phylogenetic network. | here | 3.6.0 | |||
| Uses Gibbs Sampling to explore the hypothesis of the evolutionary history from a collection of gene trees. | here | 3.6.0 | ||||
| DeepCoalCount_network | Counts the number of extra lineages contributed by a phylogenetic network and a set of gene trees. | here | 3.3.0 | |||
| DeepCoalCount_AlloppNet | Counts the number of extra lineages contributed by an allopolyploid network and a set of gene trees. | 3.8.3 | ||||
Computes the likelihood of a phylogenetic network given a collection of gene trees. | here | 3.3 | 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 the MDC criterion. | here | 3.0.0 | ||||
Detects and reconstructs horizontal gene transfer events from phylogenetic incongruence. | here | 3.0.0 | ||||
Computes the number of coalescent scenarios that can explain the incongruence observed between two trees. | here | 3.0.0 | ||||
Counts the number of extra lineages contributed by a species tree and a set of gene trees. | here | 3.0.0 | ||||
| Methods for Simulating Locus Data on Phylogenetic Networks (and Trees) | ||||||
Simulates gene trees under the multispecies network coalescent (automates the 'ms' program on an arbitrary phylogenetic network). | here | 3.6.1 | ||||
| SimBiMarkersinNetwork | Simulates bi-marker alleles under the multispecies network coalescent. | here | 3.6.1 | |||
| CoalHMM Methods | ||||||
| HmmCommand | Uses a hidden Markov to assign a species tree to each locus in data coming from a species network. | 3.5.4 | ||||
| VI_coalHMM | Black box variational inference of continuous parameters on a species tree under the coalescent with recombination using coalHMM. | 3.8.3 | ||||
| Characterizing and Comparing Phylogenetic Trees/Networks Based on Their Topologies | ||||||
Computes the phylogenetic network model.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 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 | |||||
Computes the symmetric difference, also known as the Robinson-Foulds (RF) distance, between two trees. | 3.0.0 | |||||
| SummarizeNetworks | Computes the common structures with their proportions given a set of networks (with their proportion). | here | 3.8.0 | |||