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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.

here3.6.1
MCMC_BiMarkersBayesian 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.

here3.6.0
InferNetwork_MPLInfers a phylogenetic network from gene trees under maximum pseudo-likelihood.here3.5.5
InferNetwork_ML_BootstrapInfers a phylogenetic network from gene trees under maximum likelihood with parametric bootstrap.here3.5.2
InferNetwork_ML_CVInfers a phylogenetic network from gene trees under maximum likelihood with cross-validation.here3.5.2
InferNetwork_MLInfers a phylogenetic network from gene trees under maximum likelihood.here3.4.0
InferNetwork_MPInfers a phylogenetic network from gene trees under the MDC criterion.here3.4.0
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.

here

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.

here

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.

here

3.0.0

GenCPLEX

Generates CPLEX input for a species tree and a set of gene trees.

here

3.0.0

GenST

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
CalIntroRateQuantifies the introgression probability for each reticulation branch in a given phylogenetic network.here3.6.0

ExploreHypothesis_GibbsSampling

Uses Gibbs Sampling to explore the hypothesis of the evolutionary history from a collection of gene trees.here3.6.0
DeepCoalCount_networkCounts the number of extra lineages contributed by a phylogenetic network and a set of gene trees.here3.3.0

CalGTProb

Computes the likelihood of a phylogenetic network given a collection of gene trees.

here

3.3.0

ProcessGT

Refines and roots gene trees with respect to a rooted binary species tree under the MDC criterion.

here

3.0.0

RIATAHGT

Detects and reconstructs horizontal gene transfer events from phylogenetic incongruence.

here

3.0.0

CountCoal

Computes the number of coalescent scenarios that can explain the incongruence observed between two trees.

here

3.0.0

DeepCoalCount_tree

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)

SimGTinNetwork

Simulates gene trees under the multispecies network coalescent (automates the 'ms' program on an arbitrary phylogenetic network).

here

3.6.1

SimBiMarkersinNetworkSimulates bi-marker alleles under the multispecies network coalescent.here3.6.1
CoalHMM Methods
HmmCommandUses a hidden markov to assign a species tree to each locus in data coming from a species network. 3.5.4
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

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