Phylogenetic reconstruction from arbitrary gene-order data

Jijun Tang, Bernard M.E. Moret, Liying Cui, Claude Walker Depamphilis

Research output: Chapter in Book/Report/Conference proceedingConference contribution

23 Scopus citations

Abstract

Phylogenetic reconstruction from gene-order data has attracted attention from both biologists and computer scientists over the last few years. So far, our software suite GRAPPA is the most accurate approach, but it requires that all genomes have identical gene content, with each gene appearing exactly once in each genome. Some progress has been made in handling genomes with unequal gene content, both in terms of computing pairwise genomic distances and in terms of reconstruction. In this paper, we present a new approach for computing the median of three arbitrary genomes and apply it to the reconstruction of phytogenies from arbitrary gene-order data. We implemented these methods within GRAPPA and tested them on simulated datasets under various conditions as well as on a real dataset of chloroplast genomes; we report the results of our simulations and our analysis of the real dataset and compare them to reconstructions made by using neighbor-joining and using the original GRAPPA on the same genomes with equalized gene contents. Our new approach is remarkably accurate both in simulations and on the real dataset, in contrast to the distance-based approaches and to reconstructions using the original GRAPPA applied to equalized gene contents.

Original languageEnglish (US)
Title of host publicationProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
Pages592-599
Number of pages8
StatePublished - Sep 24 2004
EventProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 - Taichung, Taiwan, Province of China
Duration: May 19 2004May 21 2004

Publication series

NameProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Other

OtherProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
CountryTaiwan, Province of China
CityTaichung
Period5/19/045/21/04

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All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Tang, J., Moret, B. M. E., Cui, L., & Depamphilis, C. W. (2004). Phylogenetic reconstruction from arbitrary gene-order data. In Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 (pp. 592-599). (Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004).