Abstract
Motivation:
Missing data and incomplete lineage sorting (ILS) are two major obstacles to accurate species tree inference. Gene tree summary methods such as ASTRAL and ASTRID have been developed to account for ILS. However, they can be severely affected by high levels of missing data.
Results:
We present Asteroid, a novel algorithm that infers an unrooted species tree from a set of unrooted gene trees. We show on both empirical and simulated datasets that Asteroid is substantially more accurate than ASTRAL and ASTRID for very high proportions (>80%) of missing data. Asteroid is several orders of magnitude faster than ASTRAL for datasets that contain thousands of genes. It offers advanced features such as parallelization, support value computation and support for multi-copy and multifurcating gene trees.
Missing data and incomplete lineage sorting (ILS) are two major obstacles to accurate species tree inference. Gene tree summary methods such as ASTRAL and ASTRID have been developed to account for ILS. However, they can be severely affected by high levels of missing data.
Results:
We present Asteroid, a novel algorithm that infers an unrooted species tree from a set of unrooted gene trees. We show on both empirical and simulated datasets that Asteroid is substantially more accurate than ASTRAL and ASTRID for very high proportions (>80%) of missing data. Asteroid is several orders of magnitude faster than ASTRAL for datasets that contain thousands of genes. It offers advanced features such as parallelization, support value computation and support for multi-copy and multifurcating gene trees.
Original language | English |
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Article number | btac832 |
Number of pages | 8 |
Journal | Bioinformatics |
Volume | 39 |
Issue number | 1 |
DOIs | |
Publication status | Published - 1 Jan 2023 |
Bibliographical note
Funding Information:This work was financially supported by the Klaus Tschira Foundation and by DFG grant STA 860/6-2. T.A.W. was supported by a Royal Society University Fellowship. This work was funded by the Gordon and Betty Moore Foundation [GBMF9741 to T.A.W.].
Publisher Copyright:
© The Author(s) 2022. Published by Oxford University Press.