TriL2Net: Constructing level-2 phylogenetic networks from trinets, by Sjors Kole (thesis)
Finding the temporal hybridization number for sets of phylogenetic trees, by Sander Borst (thesis)
Computing Optimal Tree-Child Networks for Sets of Binary Phylogenetic Trees, by Norbert Zeh (paper)
Treeduce: A preprocessing algorithm for Hybridization Number on any number of binary or nonbinary trees. (paper)
NonbinaryCycleKiller: A practical algorithm for constructing a phylogenetic network from two large (possibly multifurcating) trees. (paper)
ILPEACE: Reconciling a binary gene tree with a binary undated species tree. (paper)
MPNet: Computing the Maximum Parsimony score of a phylogenetic NETwork. (paper)
MAF: Maximum Agreement Forests for nonbinary trees. (paper)
CycleKiller: A practical algorithm for constructing a phylogenetic network from two large bifurcating trees. By Steven Kelk. (paper)
Cass: Integrated into Dendroscope. Combines any set of phylogenetic trees into a phylogenetic network representing all clusters of all input trees. (paper) (user Guide).
LEV1ATHAN: A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. Combines any set of phylogenetic trees into a level-1 phylogenetic network (a galled tree) that is consistent with a large number of the triplet topologies of the input trees. By Steven Kelk. (paper)
SIMPLISTIC: Constructs level-k phylogenetic networks from triplets. This program always returns a phylogenetic network consistent with all input triplets. By Steven Kelk. Partly based on the SL-k and MINPITS algorithms in this paper.
MARLON: Constructs a level-1 phylogenetic network with a minimum number of reticulations consistent with a dense set of triplets, if such a network exists. By Steven Kelk. (paper)
LEVEL2: Constructs a level-2 phylogenetic network consistent with a dense set of triplets, if such a network exists. By Steven Kelk. (paper)
Cass, Simplistic and various other phylogenetic network methods can be found in the user-friendly software package Dendroscope.