Simplifying gene trees for easier comprehension.

BMC Bioinformatics
Paul-Ludwig LottGeorg Fuellen

Abstract

In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important. 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 protei...Continue Reading

References

Jan 5, 2001·Nucleic Acids Research·T Sicheritz-Pontén, S G Andersson
Jul 10, 2001·Journal of Molecular Evolution·L B Koski, G B Golding
Jul 21, 2001·Stem Cells·M Pesce, H R Schöler
Dec 26, 2001·Bioinformatics·G FuellenR Giegerich
Dec 26, 2001·Nucleic Acids Research·David L WheelerBarbara A Rapp
Dec 26, 2001·Nucleic Acids Research·Hester M WainSue Povey
May 1, 2004·BMC Bioinformatics·Timothy HughesDavid A Liberles
Oct 2, 2004·Nucleic Acids Research·Tancred Frickey, Andrei N Lupas
May 18, 2010·Bioinformatics·Thomas Junier, Evgeny M Zdobnov

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Citations

Oct 13, 2006·BMC Bioinformatics·François ChevenetRichard Christen
May 9, 2007·BMC Bioinformatics·Bengt SennbladLars Arvestad
Dec 31, 2015·BMC Bioinformatics·Christian AllendeCedric Little

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Software Mentioned

Walrus
RiPE
TreeSimplifier
RiPE Retrieval - induced Phylogeny Environment
HUGO
pyphy
Hypertree
RiPE ( Retrieval - induced Phylogeny Environment )
phylome

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