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 | Bayesian MCMC posterior estimation of phylogenetic networks and gene trees on sequences from multiple independent loci. | here | 3.6.1 | ||
MCMC_BiMarkers | Bayesian estimation of the posterior distribution of phylogenetic networks given bi-allelic genetic markers (SNPs, AFLPs, etc). | here | 3.6.1 | ||
MCMC_GT | Bayesian MCMC posterior estimation of phylogenetic networks 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 | 3.6.4 | ||
InferNetwork_MPL | Infers a phylogenetic network from gene trees under maximum pseudo-likelihood. | here | 3.5.5 | ||
InferNetwork_ML_Bootstrap | Infers a phylogenetic network from gene trees under maximum likelihood with parametric bootstrap. | here | 3.5.2 | ||
InferNetwork_ML_CV | Infers a phylogenetic network from gene trees under maximum likelihood with cross-validation. | here | 3.5.2 | ||
InferNetwork_ML | Infers a phylogenetic network from gene trees under maximum likelihood. | here | 3.4.0 | ||
InferNetwork_MP | Infers a phylogenetic network from gene trees under the MDC criterion. | here | 3.4.0 | ||
InferNetwork_MP_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 | |||||
Computes the trees, tripartitions and clusters contained in a phylogenetic network. | |||||
Computes the distance between two phylogenetic networks based on their topologies. | |||||
Computes the number of coalescent scenarios that can explain the incongruence observed between two trees. | |||||
Count the number of extra lineages contributed by a species tree and a set of gene trees. | |||||
Generates CPLEX input for a species tree and a set of gene trees. | |||||
Generates species tree topologies based on maximal sets of compatible clusters. | |||||
Infers the a species tree using bootstrap with existing | 3.0.0 | ||||
Infer the Infers a species tree from gene trees using the "Democratic Vote" method. | 3.0.0 | ||||
Infer the Infers a species tree by GLASS.using the GLASS method of Mossel and Roch. | here | 3.0.0 | |||
Infer the Infers a species tree from gene trees using an extended version of Majority Consensus which can deal with gene trees having greedy consensus (allows for gene trees with multiple alleles in species and for unrooted gene trees). | 3.0.0 | ||||
Infer the Infers a species tree from gene tree topologies using the “Minimize Deep Coalescence” (MDC) criterion. | here | 3.0.0 | |||
Infer the species tree using MDC criterion but also considering time. | |||||
Computes the least common ancestor of a group of nodes in a tree. | |||||
Computes a Maximum Agreement Subtree of a pair of trees. | |||||
Infers a species tree from gene trees with coalescent times using the MDC criterion. | 3.0.0 | ||||
Infers a species tree from unrooted gene 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 | |||
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 | 3.3.0 | |||
Refines and roots | Refine and root 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 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 |