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Related Concept Videos

Phylogenetic Trees03:21

Phylogenetic Trees

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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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Updated: Oct 31, 2025

A Practical Guide to Phylogenetics for Nonexperts
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Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.

Luna L Sánchez-Reyes1, Martha Kandziora2,3, Emily Jane McTavish2

  • 1School of Natural Sciences, University of California, Merced, USA. lsanchezreyes2@ucmerced.edu.

BMC Bioinformatics
|June 30, 2021
PubMed
Summary
This summary is machine-generated.

Physcraper automates updating phylogenetic trees with new DNA data, simplifying comparisons for biologists. This open-source tool aids both specialists and non-specialists in phylogenetic analysis.

Keywords:
DNA alignmentGene phylogenyGene treeInteroperabilityMultilocusOpen Tree of LifeOpen scienceOtolPublic databaseReproducibility

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Area of Science:

  • * Evolutionary biology
  • * Bioinformatics

Background:

  • * Phylogenetic reconstruction is crucial in biology but complex for non-specialists.
  • * Existing tools automate matrix assembly but not result interpretation or comparison.
  • * Difficulties arise in comparing phylogenies and selecting them for further analysis.

Purpose of the Study:

  • * To introduce Physcraper, a Python program automating phylogenetic tree updates.
  • * To facilitate comparison of published phylogenies with their updated versions.
  • * To provide a tool for generating phylogenetic hypotheses from public data.

Main Methods:

  • * Physcraper is a command-line Python program.
  • * It updates published phylogenies by incorporating public DNA sequences into alignments.
  • * Utilizes Open Tree of Life project tools for taxonomic linking and database comparison.

Main Results:

  • * Automates updating published phylogenies with new DNA sequence data.
  • * Enables straightforward comparison of original and updated phylogenetic trees.
  • * Supports non-specialists in generating phylogenetic hypotheses from expert knowledge.

Conclusions:

  • * Physcraper promotes open science and data sharing in phylogenetics.
  • * The tool is cross-platform and released under an open-source license.
  • * Comprehensive documentation is available for installation and usage.