Joint amalgamation of most parsimonious reconciled gene trees

• DOI: 10.1093/bioinformatics/btu728
• Publication Date: 2014-11-08T01:28:35Z
• Authors: Celine Scornavacca; Edwin Jacox; Gergely J. Szöllősi
• Keywords: Tera-; Tree (set theory); Maximum parsimony; Sequence (biology)

Abstract Motivation: Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods incorporated species phylogeny in tree reconstruction, leading dramatic improvements accuracy. Although probabilistic are able estimate all model parameters but computationally expensive, parsimony methods—generally more efficient—require a prior and statistical support. Results: Here, we present Tree Estimation using Reconciliation (TERA) algorithm, based, aware method for reconstruction based scoring scheme combining duplication, transfer loss costs with an sequence likelihood. TERA explores reconciled trees that can be amalgamated from sample trees. Using large scale simulated dataset, demonstrate achieves same accuracy as corresponding while being faster, outperforms other parsimony-based both speed. Running set 1099 homologous families complete cyanobacterial genomes, find incorporating knowledge results two thirds reduction number apparent events. Availability implementation: The algorithm is implemented our program TERA, which freely available http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA. Contact: [e-mail], [e-mail] Supplementary information: data at Bioinformatics online.