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相关概念视频

Phylogenetic Trees03:21

Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
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The human bronchi and bronchial tree play a crucial role in the respiratory system, facilitating the exchange of oxygen and carbon dioxide. Let's delve into the intricate structure and functions of these respiratory components.
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The parallel RLC circuit is an arrangement where the resistor (R), inductor (L), and capacitor (C) are all connected to the same nodes and, as a result, share the same voltage across them. The parallel RLC circuit is analyzed in terms of admittance (Y), which reflects the ease with which current can flow. The admittance is given by:
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The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
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A Practical Guide to Phylogenetics for Nonexperts
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比特可复制的并行类遗传树推理推理

Christoph Stelz1, Lukas Hübner1,2, Alexandros Stamatakis1,2,3

  • 1Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Germany.

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概括
此摘要是机器生成的。

在平行基因推断中浮点圆形化错误导致进化树结果中的显著差异. 这项研究介绍了ReproRed,这是一种新型的减少算法,也是第一个用于准确的基因分析的比特可重现工具.

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科学领域:

  • 计算生物学 计算生物学
  • 生物信息学是一种生物信息学.
  • 进化生物学 进化生物学

背景情况:

  • 遗传学树使用基因组数据重建进化历史.
  • 最大概率 (ML) 推断方法被广泛用于遗传学分析.
  • 在ML推理中的并行计算引入了由于浮点算法而导致的圆形化错误,影响了结果.

研究的目的:

  • 调查并行计算对ML遗传学推理可重现性的影响.
  • 开发一种方法来实现可比特复制的结果,并行进行基因组学分析.
  • 介绍可重复的并行减少操作的一般算法.

主要方法:

  • 开发了ReproRed减少算法,以保持固定的操作顺序,独立于并行执行模式.
  • 将ReproRed集成到RAxML-NG中,这是一个广泛使用的家族遗传推断工具,以创建一个可以复制的比特版本.
  • 在实证数据集上评估了ReproRed算法和增强的RAxML-NG的性能和可重现性.

主要成果:

  • 不同的并行性导致超过31%的测试数据集的遗传树搜索分歧.
  • 8%的不同数据集在统计学上显著地产生了比最知名的ML树更糟糕的树.
  • 用ReproRed增强的RAxML-NG在768个核心上实现了位可重现的结果,性能减慢最小 (中位数为0.8%).

结论:

  • 在平行基因推断中非可复制性是一个影响进化分析的重要问题.
  • ReproRed为可重复的关联并行减少操作提供了一个通用的解决方案,它不仅适用于遗传学.
  • 开发的可位复制的RAxML-NG工具确保了在不同的计算环境中可靠的基因推断.