Abstract
Background: In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability. Results: The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in O(n2) time by querying at most (n - 4) log(n - 1) quartet topologies, where n is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a probability approximately 1 - p in O(n4log n) time, where p is the probability for a quartet topology being an error. This probability is improved by the third algorithm to approximately 1/1+q2+1/2q4 +1/16q5, where q=p/1-p with running time of O(n5), which is at least 0.984 when p < 0.05. Conclusion: The three proposed algorithms are mathematically guaranteed to reconstruct the "true " phylogeny with a high success probability. The experimental results showed that the third algorithm produced phylogenies with a higher probability than its aforementioned theoretical lower bound and outperformed some existing phylogeny reconstruction methods in both speed and accuracy.
| Original language | English (US) |
|---|---|
| Article number | 1 |
| Journal | Algorithms for Molecular Biology |
| Volume | 3 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 24 2008 |
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ASJC Scopus subject areas
- Computational Theory and Mathematics
- Applied Mathematics
- Molecular Biology
- Structural Biology
Cite this
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Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability. / Wu, Gang; Kao, Ming-Yang; Lin, Guohui; You, Jia Huai.
In: Algorithms for Molecular Biology, Vol. 3, No. 1, 1, 24.01.2008.Research output: Contribution to journal › Article
TY - JOUR
T1 - Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability
AU - Wu, Gang
AU - Kao, Ming-Yang
AU - Lin, Guohui
AU - You, Jia Huai
PY - 2008/1/24
Y1 - 2008/1/24
N2 - Background: In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability. Results: The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in O(n2) time by querying at most (n - 4) log(n - 1) quartet topologies, where n is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a probability approximately 1 - p in O(n4log n) time, where p is the probability for a quartet topology being an error. This probability is improved by the third algorithm to approximately 1/1+q2+1/2q4 +1/16q5, where q=p/1-p with running time of O(n5), which is at least 0.984 when p < 0.05. Conclusion: The three proposed algorithms are mathematically guaranteed to reconstruct the "true " phylogeny with a high success probability. The experimental results showed that the third algorithm produced phylogenies with a higher probability than its aforementioned theoretical lower bound and outperformed some existing phylogeny reconstruction methods in both speed and accuracy.
AB - Background: In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability. Results: The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in O(n2) time by querying at most (n - 4) log(n - 1) quartet topologies, where n is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a probability approximately 1 - p in O(n4log n) time, where p is the probability for a quartet topology being an error. This probability is improved by the third algorithm to approximately 1/1+q2+1/2q4 +1/16q5, where q=p/1-p with running time of O(n5), which is at least 0.984 when p < 0.05. Conclusion: The three proposed algorithms are mathematically guaranteed to reconstruct the "true " phylogeny with a high success probability. The experimental results showed that the third algorithm produced phylogenies with a higher probability than its aforementioned theoretical lower bound and outperformed some existing phylogeny reconstruction methods in both speed and accuracy.
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UR - http://www.scopus.com/inward/citedby.url?scp=40649125833&partnerID=8YFLogxK
U2 - 10.1186/1748-7188-3-1
DO - 10.1186/1748-7188-3-1
M3 - Article
C2 - 18218120
AN - SCOPUS:40649125833
VL - 3
JO - Algorithms for Molecular Biology
JF - Algorithms for Molecular Biology
SN - 1748-7188
IS - 1
M1 - 1
ER -