**Computing Optimal Tree-Child Networks for Sets of Binary Phylogenetic Trees**: the algorithm from this paper.

**Treeduce**: A preprocessing algorithm for Hybridization Number on any number of binary or nonbinary trees. See the paper.

**NonbinaryCycleKiller**: A practical algorithm for constructing a phylogenetic network from two large (possibly multifurcating) trees. See the paper.

**ILPEACE**: Reconciling a binary gene tree with a binary undated species tree, see the paper.

**MPNet**: Computing the Maximum Parsimony score of a phylogenetic NETwork, see the paper.

**MAF**: Maximum Agreement Forests for nonbinary trees, see the paper.

**CycleKiller**: A practical algorithm for constructing a phylogenetic network from two large bifurcating trees. The number of reticulations is very close to the minimum, see the paper.

**Cass**: Integrated into Dendroscope. Combines any set of phylogenetic trees into a phylogenetic network representing all clusters of all input trees. CASS uses significanly fewer reticulations than other methods. 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. Paper. **Download**.

**SIMPLISTIC**: Constructs level-*k* phylogenetic networks from triplets. This program always returns a phylogenetic network consistent with all input triplets. Partly based on the SL-*k* and MINPITS algorithms in this paper. **Download**.

**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. Paper. **Download**.

**LEVEL2**: Constructs a level-2 phylogenetic network consistent with a dense set of triplets, if such a network exists. Paper. **Download**.

Cass, Simplistic and various other phylogenetic network methods can be found in the user-friendly software package Dendroscope.