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Related Concept Videos

Phylogeny01:23

Phylogeny

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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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A Practical Guide to Phylogenetics for Nonexperts
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Poplar: a phylogenomics pipeline.

Elizabeth Koning1,2, Arjun Subedi1,3, Raga Krishnakumar1

  • 1Biosecurity and Bioassurance Department, Sandia National Laboratories, Livermore, CA 94550, United States.

Bioinformatics Advances
|June 13, 2025
PubMed
Summary
This summary is machine-generated.

Poplar is a new computational pipeline that simplifies the generation of phylogenomic trees from genomic data. This tool streamlines complex analyses, making species tree construction more accessible for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenomic tree generation is crucial for understanding biological systems.
  • Existing methods involve complex, multi-step processes with significant scientific and technical challenges.
  • Obtaining genomic data is increasingly accessible, highlighting the need for streamlined analysis tools.

Purpose of the Study:

  • To present Poplar, a novel computational pipeline designed to simplify and streamline the construction of phylogenomic trees.
  • To address the computational and logistical challenges associated with phylogenomic analyses.
  • To provide a user-friendly framework for generating species trees from genomic data.

Main Methods:

  • Poplar is a computational pipeline implemented in Python and supported on Linux.
  • It integrates state-of-the-art software for essential phylogenomic analysis steps.
  • The pipeline operates directly on genomic data, with or without annotations, and does not require external databases.

Main Results:

  • Poplar successfully generates species trees that closely align with published state-of-the-art trees.
  • The pipeline enables parallel execution for enhanced performance on clusters and cloud computing environments.
  • Poplar offers a significantly simpler and faster alternative to manual phylogenomic pipeline execution.

Conclusions:

  • Poplar effectively streamlines the complex process of phylogenomic tree construction.
  • The pipeline enhances accessibility and efficiency for researchers in bioinformatics and computational biology.
  • Poplar is freely available on GitHub, promoting wider adoption and use in biological research.