Joint amalgamation of most parsimonious reconciled gene trees. Results: Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication, transfer and loss costs with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that can be amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate that TERA achieves the same accuracy as the corresponding probabilistic method while being faster, and outperforms other parsimony-based methods in both accuracy and speed. Running TERA on a set of 1099 homologous gene families from complete cyanobacterial genomes, we find that incorporating knowledge of the species tree results in a two thirds reduction in the number of apparent transfer events. Availability and implementation: The algorithm is implemented in our program TERA, which is freely available from http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA.
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References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- Chauve, Cedric; Ponty, Yann; Wallner, Michael: Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models (2020)
- Dinh, Vu; Ho, Lam Si Tung; Suchard, Marc A.; Matsen, Frederick A. IV: Consistency and convergence rate of phylogenetic inference via regularization (2018)
- Chan, Yao-ban; Ranwez, Vincent; Scornavacca, Céline: Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations (2017)
- Chauve, Cedric; Jones, Mark; Lafond, Manuel; Scornavacca, Céline; Weller, Mathias: Constructing a consensus phylogeny from a leaf-removal distance (extended abstract) (2017)