GeneTree is a program used for comparing gene and species trees using reconciled trees. So this can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplication and losses, and search for optimal species trees.
Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories.
This anomaly can arise from horizontal transfer such as hybridization, lineage sorting, and gene duplication and extinction.
Lineage sorting could also be termed as deep coalescence, the failure of ancestral copies to coalesce into a common ancestral copy until deeper than previous speciation events.
These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size).
A similar dependence on process is found in historical biogeography and host-parasite relationships.
Each of the processes of discord could yield a different parsimony criterion for reconstructing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events.
Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the probability that a particular gene tree would occur given a species tree
You can download free version of Genetree
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