PhyloNet

PhyloNet is a handy, easy to use tool specially designed to offer users a suite of tools for reconstructing and analyzing reticulate (non-treelike) evolutionary relationships. In particular, the software package includes features for inferring horizontal gene transfer from a pair of species/gene trees, and detecting interspecific recombination breakpoints in a sequence alignment.

Further, it has the capabilities for reading/storing phylogenetic networks, and comparing phylogenetic networks topologies. As the algorithms for phylogenetic network Reconstruction and evaluation make use of algorithmic techniques from the domain of phylogenetic trees, the package also contains several tree-oriented features, such as modules for computing the maximum agreement subtrees, the Robinson-Foulds distance measures, etc.

Here are some key features of "PhyloNet":

· MAST - Maximum Agreement Subtree
· RF - Robinson-Foulds/Symmetric Difference tree measure
· RIATAHGT - a heuristic for detecting HGT events from a pair of species/gene trees
· LCA - least common ancestor of a set of nodes in a tree
· RECOMP - a window-based method for detecting interspecific recombination breakpoints
· CHARNET - a tool for computing clusters, trees and tripartitions in a network
· CMPNETS - a tool for computing the distance Between two networks
· NETPARS - a tool for scoring the parsimony of phylogenetic networks
· COUNTCOAL - a tool for enumerating all valid coalescent scenarios of a gene within the branches of a species tree
· GENCPLEX - a tool for generating an MILP formulation that can be solved by CPLEX for a species trees and a set of gene trees
· GENST - a tool for generating species tree topoloties based on maximal sets of compatible clusters.
· COMPUTE_ST (this tool is a Perl script) - for reconstructing the species tree from gene trees under the coalescent.