Charnet

Computes the trees, tripartitions and clusters contained in a phylogenetic network.

Cmpnets

Computes the distance between two phylogenetic networks based on their topologies.

CountCoal

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

DeepCoalCount

Counts the number of extra lineages contributed by a species tree and a set of gene trees.

GenCPLEX

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

GenST

Generates species tree topologies based on maximal sets of compatible clusters.

Infer_ST_Bootstrap

Infers the species tree using bootstrap with existing Infer_ST commands.

Infer_ST_DV

Infers the species tree from gene trees using Democratic Vote.

Infer_ST_GLASS

Infers the species tree by GLASS.

Infer_ST_MC

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.

Infer_ST_MDC

Infers the species tree using the “Minimize Deep Coalescence” (MDC) criterion.

Infer_ST_MDC_Time

Infers the species tree using MDC criterion but also considering time.

Infer_ST_MDC_UR

Infers the species tree from unrooted gene trees using MDC criterion.

LCA

Computes the least common ancestor of a group of nodes in a tree.

MAST

Computes a Maximum Agreement Subtree of a pair of trees.

ProcessGT

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

RIATAHGT

Detects and reconstructs horizontal gene transfer events from phylogenetic incongruence.

Sim_GTinNetwork

Simulates gene trees under the phylogenetic network model.

SymmetricDifference

Computes the symmetric difference, also known as the Robinson-Foulds (RF) distance, between two trees.

CalGTProb

Computes the probability of a gene tree topology within a phylogenetic network.