ArticleAlgorithms for molecular biology : AMB2018
OCTAL: Optimal Completion of gene trees in polynomial time.
Article in Algorithms for molecular biology : AMB, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review.Ecology and evolution · 2024Review
- Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination.PLoS computational biology · 2022Article
- PhyloMissForest: a random forest framework to construct phylogenetic trees with missing data.BMC genomics · 2022Article
- Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices.BMC genomics · 2020Article
- Forcing external constraints on tree inference using ASTRAL.BMC genomics · 2020Article
- Non-parametric correction of estimated gene trees using TRACTION.Algorithms for molecular biology : AMB · 2020Article
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Authors and funding
4 authors.
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Abstract
backgroundFor a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain all of the species of interest. As incomplete gene trees can impact downstream analyses, accurate completion of gene trees is desirable.
resultsWe introduce the
conclusionsOCTAL is a useful technique for adding missing taxa to incomplete gene trees and provides good accuracy under a wide range of model conditions. However, results show that OCTAL's accuracy can be reduced when incomplete lineage sorting is high, as the reference tree can be far from the true gene tree. Hence, this study suggests that OCTAL would benefit from using other types of reference trees instead of species trees when there are large topological distances between true gene trees and species trees.
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