MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.
MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.
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DOI：
10.1186/s12862-018-1131-3
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发表时间：
2018-02-02
影响因子：
3.4
通讯作者：
Minh BQ
中科院分区：
文献类型：
--
作者：
Hoang DT;Vinh LS;Flouri T;Stamatakis A;von Haeseler A;Minh BQ
非参数bootstrap方法被广泛用于系统发生树的分支支持度的度量。然而，自举是计算昂贵的，仍然是系统发育分析的瓶颈。最近，提出了一种用于最大似然分析的超快自举近似（UFBoot）方法。然而，这种方法仍然是最大的吝啬失踪。为了缩小这一差距，我们提出了MPBoot，UFBoot的适应和扩展计算分支支持下的最大简约原则。MPBoot适用于统一和非统一成本矩阵。我们对生物DNA和蛋白质的分析表明，在统一的成本矩阵下，MPBoot运行平均比PAUP* 中实现的标准简约引导快4.7（DNA）至7倍（蛋白质数据）（范围：1.2-20.7）;但比TNT中快速搜索例程的标准引导慢1.6（DNA）至4.1倍（蛋白质数据）（fast-TNT）。然而，对于非均匀成本矩阵，MPBoot比fast-TNT快5（DNA）到13倍（蛋白质数据）（范围：0.3-63.9）。我们注意到MPBoot比PAUP* 和fast-TNT更频繁地获得更好的分数。然而，如果在TNT中调用密集但较慢的搜索，则这种效果不太明显。此外，大规模模拟数据的实验表明，虽然PAUP* 和TNT自助估计过于保守，MPBoot自助估计似乎更无偏。MPBoot提供了一个有效的替代标准的最大简约引导过程。它表现出良好的性能方面的运行时间，找到一个最大的简约树的能力，以及模拟和经验数据集的高引导精度。MPBoot易于使用，开源，可在http://www.cibiv.at/software/mpboot上获得。本文的在线版本（10.1186/s12862-018-1131-3）包含补充材料，可供授权用户使用。
The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony. To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2–20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3–63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased. MPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot. The online version of this article (10.1186/s12862-018-1131-3) contains supplementary material, which is available to authorized users.
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影响因子：
10.7
作者：
Minh BQ;Nguyen MA;von Haeseler A
通讯作者：
von Haeseler A
影响因子：
10.7
作者：
Wilkinson, M
通讯作者：
Wilkinson, M
DOI：
10.1111/j.1096-0031.1996.tb00196.x
发表时间：
1994-09-01
期刊：
CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY
影响因子：
--
作者：
FARRIS, JS;KALLERSJO, M;BULT, C
通讯作者：
BULT, C
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ
影响因子：
10.7
作者：
Hoang DT;Chernomor O;von Haeseler A;Minh BQ;Vinh LS
通讯作者：
Vinh LS