Related Experiment Video
Updated: Jan 1, 2026
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
36.0K
EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
Chandler D Gatenbee1, Ryan O Schenck1,2, Rafael R Bravo1
1Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, 33612, FL, USA.
BMC Bioinformatics
|December 18, 2019
Summary
EvoFreq is a new R package that visualizes clonal evolutionary dynamics. It helps track changes in genotype frequencies over time for high-throughput sequence data analysis.
Area of Science:
- Population Genetics
- Evolutionary Biology
- Bioinformatics
Background:
- High-throughput sequencing generates extensive molecular data for population characterization.
- Analyzing genotype frequency changes over time reveals population evolutionary dynamics.
- Visualizing complex, time-series population data requires flexible and user-friendly tools.
Purpose of the Study:
- To introduce EvoFreq, a comprehensive R package for visualizing evolutionary and population frequency dynamics.
- To provide methods for analyzing clonal dynamics at single time points or over extended periods.
- To offer enhanced visualization capabilities beyond existing tools for sequence or model data.
Main Methods:
- Implementation in R, emphasizing user options and minimal dependencies.
- Development of a toolset for high-throughput visualization of clonal and temporal dynamics.
- Integration of various informative methods for displaying population frequency data.
Main Results:
- EvoFreq provides a comprehensive suite of tools for visualizing evolutionary dynamics.
- The package facilitates the analysis of clonal frequencies, both statically and over time.
- EvoFreq offers expanded visualization options compared to previous methods.
Conclusions:
- EvoFreq offers a high-throughput method for analyzing temporal dynamics of hereditary information.
- The R package is designed for rapid building and interrogation of evolutionary data across diverse systems.
- EvoFreq is freely accessible, promoting broad adoption in evolutionary and population genetics research.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.8K
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...
6.8K
02:05Gene Evolution - Fast or Slow?
7.9K
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.
In contrast, regions which code...
In contrast, regions which code...
7.9K
02:05Gene Evolution - Fast or Slow?
3.3K
3.3K
01:07Speciation Rates
22.5K
Overview
22.5K
01:09Mutation, Gene Flow, and Genetic Drift
61.6K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
61.6K
01:14Relative Frequency Histogram
6.3K
The relative frequency depicts the proportion of data points that have each value. The frequency tells the number of data points that have each value. Like the histogram, a relative frequency histogram also has the same shape with a horizontal scale (the x-axis), but the vertical scale (the y-axis) is marked with relative frequencies (percentages of the whole) instead of actual frequencies. A relative frequency histogram is a graphical representation of a frequency distribution where the...
6.3K