Simplifying gene trees for easier comprehension

We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tree to a "cartoon tree" created manually, we note that both agree to a high degree.Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families. The software is available at http://www.uni-muenster.de/Bioinformatics/services/treesim/ webcite.The large number of ongoing genome and EST (expressed sequence tag) sequencing projects provides a massively increasing amount of protein data. The physiological role and function of almost all proteins identified by these projects is not known. Due to the large number of newly identified proteins, it is not possible to annotate their function using conventional experimental approaches or manual data analysis, as demonstrated by any paper reporting a newly sequenced organism. Since the 1970s numerous tools have been developed in order to perform automated analyses of sequence data and to annotate functions of proteins based on these analyses. The interpretation of results derived from these automated analyses is also a daunting task due to the complexity of the information revealed.Phylogeneti