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• W4213115383 abstract "Abstract Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive to hard-to-avoid errors introduced in the gene tree estimation step. This dilemma has created much debate on the merits of concatenation versus summary methods and practical obstacles to using summary methods more widely and to the exclusion of concatenation. The most successful attempt at making summary methods resilient to noisy gene trees has been contracting low support branches from the gene trees. Unfortunately, this approach requires arbitrary thresholds and poses new challenges. Here, we introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the original ASTRAL. More consequentially, weighting dramatically improves accuracy in a wide range of simulations and reduces the gap with concatenation in conditions with low gene tree discordance and high noise. On empirical data, weighting improves congruence with concatenation and increases support. Together, our results show that weighting, enabled by a new optimization algorithm we introduce, dramatically improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines." @default.
• W4213115383 created "2022-02-24" @default.
• W4213115383 creator A5016903406 @default.
• W4213115383 creator A5087959579 @default.
• W4213115383 date "2022-02-20" @default.
• W4213115383 modified "2023-10-16" @default.
• W4213115383 title "Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees" @default.
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• W4213115383 cites W1683278196 @default.
• W4213115383 cites W1856776018 @default.
• W4213115383 cites W1886547141 @default.
• W4213115383 cites W1889423108 @default.
• W4213115383 cites W1924404512 @default.
• W4213115383 cites W1929783548 @default.
• W4213115383 cites W1981509964 @default.
• W4213115383 cites W1999083683 @default.
• W4213115383 cites W2011606533 @default.
• W4213115383 cites W2020697299 @default.
• W4213115383 cites W2031611770 @default.
• W4213115383 cites W2032016329 @default.
• W4213115383 cites W2037654474 @default.
• W4213115383 cites W2038370559 @default.
• W4213115383 cites W2052432722 @default.
• W4213115383 cites W2054652527 @default.
• W4213115383 cites W2060425093 @default.
• W4213115383 cites W2063345613 @default.
• W4213115383 cites W2066327035 @default.
• W4213115383 cites W2083015817 @default.
• W4213115383 cites W2105541048 @default.
• W4213115383 cites W2108039804 @default.
• W4213115383 cites W2119837484 @default.
• W4213115383 cites W2120323779 @default.
• W4213115383 cites W2121633897 @default.
• W4213115383 cites W2125024684 @default.
• W4213115383 cites W2126325593 @default.
• W4213115383 cites W2131944877 @default.
• W4213115383 cites W2139478957 @default.
• W4213115383 cites W2140099453 @default.
• W4213115383 cites W2141835782 @default.
• W4213115383 cites W2145562754 @default.
• W4213115383 cites W2145608399 @default.
• W4213115383 cites W2148723086 @default.
• W4213115383 cites W2151320514 @default.
• W4213115383 cites W2157552136 @default.
• W4213115383 cites W2158952520 @default.
• W4213115383 cites W2160936843 @default.
• W4213115383 cites W2162336040 @default.
• W4213115383 cites W2177087965 @default.
• W4213115383 cites W2195373932 @default.
• W4213115383 cites W2255592388 @default.
• W4213115383 cites W2277574918 @default.
• W4213115383 cites W2323303653 @default.
• W4213115383 cites W2346920492 @default.
• W4213115383 cites W2590646912 @default.
• W4213115383 cites W2601425645 @default.
• W4213115383 cites W260545600 @default.
• W4213115383 cites W2607411230 @default.
• W4213115383 cites W2771760123 @default.
• W4213115383 cites W2790050774 @default.
• W4213115383 cites W2801361050 @default.
• W4213115383 cites W2888343454 @default.
• W4213115383 cites W2897736354 @default.
• W4213115383 cites W2938111698 @default.
• W4213115383 cites W2943825966 @default.
• W4213115383 cites W2944397307 @default.
• W4213115383 cites W2949503084 @default.
• W4213115383 cites W2950847777 @default.
• W4213115383 cites W2952299127 @default.
• W4213115383 cites W2952543493 @default.
• W4213115383 cites W2953500616 @default.
• W4213115383 cites W2962714894 @default.
• W4213115383 cites W2964034570 @default.
• W4213115383 cites W2973043487 @default.
• W4213115383 cites W2981543307 @default.
• W4213115383 cites W2981705970 @default.
• W4213115383 cites W2982062771 @default.
• W4213115383 cites W2982255935 @default.
• W4213115383 cites W3005322979 @default.
• W4213115383 cites W3019023988 @default.
• W4213115383 cites W3043220456 @default.
• W4213115383 cites W3083304049 @default.
• W4213115383 cites W3085423761 @default.
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• W4213115383 doi "https://doi.org/10.1101/2022.02.19.481132" @default.
• W4213115383 hasPublicationYear "2022" @default.
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