GeneTRACE-reconstruction of gene content of ancestral species

V. Kunin, C. A. Ouzounis
2003 Bioinformatics  
Introduction Methods References GO BACK CLOSE FILE Abstract While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the
more » ... thod was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree. Abstract Introduction Methods References GO BACK CLOSE FILE (2) If a protein family is present in most of the descendants of a particular ancestor, but is not found in some subclade, the observed gene absence would normally result from gene loss. (3) Protein family distribution interspersed in distantly related clades would be indicative of horizontal gene transfer. Abstract
doi:10.1093/bioinformatics/btg174 pmid:12874054 fatcat:m6msjfqc5netjhdhkwk2jnb6ha