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Phylogenetic Trees03:21

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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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Parallel Processing01:20

Parallel Processing

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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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Updated: Jan 31, 2026

A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

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Inferencia Paralela de Árboles Filogenéticos Bit-Reproducibles

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

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

Bioinformatics (Oxford, England)
|January 30, 2026
PubMed
Resumen
Este resumen es generado por máquina.

Los errores de redondeo de punto flotante en la inferencia filogenética paralela causan discrepancias significativas en los resultados de los árboles evolutivos. Este estudio presenta ReproRed, un novedoso algoritmo de reducción y la primera herramienta bit-reproducible para un análisis filogenético preciso.

Palabras clave:
árboles filogenéticosinferencia filogenéticareproducibilidadcomputación paralelaerrores de punto flotantealgoritmo ReproRedRAxML-NGbiología computacionalbioinformáticabiología evolutiva

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Área de la Ciencia:

  • Biología Computacional
  • Bioinformática
  • Biología Evolutiva

Sus antecedentes:

  • Los árboles filogenéticos reconstruyen la historia evolutiva utilizando datos genómicos.
  • Los métodos de inferencia de Máxima Verosimilitud (ML) se utilizan ampliamente para el análisis filogenético.
  • La computación paralela en la inferencia de ML introduce errores de redondeo debido a la aritmética de punto flotante, lo que afecta los resultados.

Objetivo del estudio:

  • Investigar el impacto de la computación paralela en la reproducibilidad de la inferencia filogenética de ML.
  • Desarrollar un método para lograr resultados bit-reproducibles en análisis filogenéticos paralelos.
  • Introducir un algoritmo general para operaciones de reducción paralelas reproducibles.

Principales métodos:

  • Se desarrolló el algoritmo de reducción ReproRed para mantener un orden de operación fijo, independiente de los patrones de ejecución paralela.
  • Se integró ReproRed en RAxML-NG, una herramienta de inferencia filogenética ampliamente utilizada, para crear una versión bit-reproducible.
  • Se evaluó el rendimiento y la reproducibilidad del algoritmo ReproRed y del RAxML-NG mejorado en conjuntos de datos empíricos.

Principales resultados:

  • La variabilidad del paralelismo condujo a divergencias en las búsqueles de árboles filogenéticos en más del 31% de los conjuntos de datos probados.
  • El 8% de los conjuntos de datos divergentes produjeron árboles significativamente peores en comparación con el mejor árbol de ML conocido.
  • El RAxML-NG mejorado con ReproRed logró resultados bit-reproducibles con una mínima ralentización del rendimiento (mediana del 0,8%) en hasta 768 núcleos.

Conclusiones:

  • La no reproducibilidad en la inferencia filogenética paralela es un problema importante que afecta los análisis evolutivos.
  • ReproRed proporciona una solución general para operaciones de reducción paralelas asociativas reproducibles, aplicables más allá de la filogenética.
  • La herramienta RAxML-NG bit-reproducible desarrollada garantiza una inferencia filogenética fiable en diferentes entornos computacionales.