Name Description Since Version
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. 3.6.1
MCMC_BiMarkers Bayesian estimation of the posterior distribution of phylogenetic networks given bi-allelic genetic markers (SNPs, AFLPs, etc). 3.6.1
MCMC_GT Bayesian MCMC posterior estimation of phylogenetic networks given a list of gene tree topologies. 3.6.0
MLE_BiMarkers Maximum (pseudo-)likelihood estimation of phylogenetic networks given bi-allelic genetic markers (SNPs, AFLPs, etc). 3.6.4
InferNetwork_MPL Infers a phylogenetic network from gene trees under maximum pseudo-likelihood. 3.5.5
InferNetwork_ML_Bootstrap Infers a phylogenetic network from gene trees under maximum likelihood with parametric bootstrap. 3.5.2
InferNetwork_ML_CV Infers a phylogenetic network from gene trees under maximum likelihood with cross-validation. 3.5.2
InferNetwork_ML Infers a phylogenetic network from gene trees under maximum likelihood. 3.4.0
InferNetwork_MP Infers a phylogenetic network from gene trees under the MDC criterion. 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.
Methods for Species Tree (not Networks) Inference
Infer_ST_Bootstrap Infers a species tree using bootstrap with existing Infer_ST commands. 3.0.0
Infer_ST_DV Infers a species tree from gene trees using the "Democratic Vote" method. 3.0.0
Infer_ST_GLASS Infers a species tree using the GLASS method of Mossel and Roch. 3.0.0
Infer_ST_MC Infers a species tree from gene trees using greedy consensus (allows for gene trees with multiple alleles in species and for unrooted gene trees). 3.0.0
Infer_ST_MDC Infers a species tree from gene tree topologies using the “Minimize Deep Coalescence” (MDC) criterion. 3.0.0
Infer_ST_MDC_TIME Infers a species tree from gene trees with coalescent times using the MDC criterion. 3.0.0
Infer_ST_MDC_UR Infers a species tree from unrooted gene tree topologies using the MDC criterion. 3.0.0
GenCPLEX Generates CPLEX input for a species tree and a set of gene trees. 3.0.0
GenST Generates species tree topologies based on maximal sets of compatible clusters. 3.0.0
Methods for Analyzing Species Trees/Networks with Respect to Locus-specific Data
CallIntroRate Quantifies the introgression probability for each reticulation branch in a given phylogenetic network. 3.6.0
ExploreHypothesis_GibbsSampling Uses Gibbs Sampling to explore the hypothesis of the evolutionary history from a collection of gene trees. 3.6.0
DeepCoalCount_network Counts the number of extra lineages contributed by a phylogenetic network and a set of gene trees. 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
CalGTProb Computes the likelihood of a phylogenetic network given a collection of gene trees. 3.3.0
ProcessGT Refines and roots gene trees with respect to a rooted binary species tree under the MDC criterion. 3.0.0
RIATAHGT Infers a phylogenetic network from gene trees under the MDC criterion. 3.0.0
CountCoal Computes the number of coalescent scenarios that can explain the incongruence observed between two trees. 3.0.0
DeepCoalCount_tree Counts the number of extra lineages contributed by a species tree and a set of gene trees. 3.0.0
Methods for Simulating Locus Data on Phylogenetic Networks (and Trees)
SimGTinNetwork Simulates gene trees under the multispecies network coalescent (automates the 'ms' program on an arbitrary phylogenetic network). 3.6.1
SimBiMarkersinNetwork Simulates bi-marker alleles under the multispecies network coalescent. 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
Charnet Computes the trees, tripartitions and clusters contained in a phylogenetic network. 3.0.0
Cmpnets Computes the distance between two phylogenetic networks based on their topologies. 3.0.0
LCA Computes the least common ancestor of a group of nodes in a tree. 3.0.0
MAST Computes a Maximum Agreement Subtree of a pair of trees. 3.0.0
SymmetricDifference 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). 3.0.0