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Table 1 Main Features of the TreeSimplifier Software.

From: Simplifying gene trees for easier comprehension

Input A gene tree and a species tree. At least some of the gene names follow HUGO nomenclature (e.g. ABCC4, S100A12, POU5F1). All gene names must be supplemented with the name of the species in which the gene is found.
Output A simplified gene tree. In particular, a subtree of the gene tree such as ((human ABCC4, mouse Abcc4), fugu ABCC) is simplified to a single node "vertebrate ABCC4", because ((human, mouse), fugu) corresponds to a monophylum in species phylogeny, and gene names are consistent.
Further simplification output Further simplified gene tree: paraphyletic tree substructures such as (fly gene, (fly gene, vertebrate genes)) may be simplified to (fly gene, vertebrate genes), if gene names are consistent.
Species may be treated alike: subtrees such as (((drosophila gene, anopheles gene), drosophila gene), (anopheles gene, anopheles gene)) may be simplified to a single node "fly genes" if both flies are to be treated alike and gene names are consistent.
GUI extras Hyperbolic tree browsing, searching for text in the tree.