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On this page
  • Alignments & Sequences
  • Phylogenetic Trees

Image Gallery¶

We use Plotly as our backend for visualisation. It provides excellent graph interactivity in Jupyter notebooks.

Alignments & Sequences¶

  • Sequence Features
    • Drawing all features on a sequence segment
    • Drawing selected feature biotypes
  • Sequence logos
    • Drawing logo for a TFBS
    • Drawing a sequence logo from a multiple sequence alignment
    • Sequence logo of protein alignment
  • Information analysis of an alignment
    • Illustrated with a simple example
    • On a sample data set
  • Counting gaps per sequence
    • Plotting counts of unique gaps
    • Displaying unique gaps as a bar chart
    • Displaying unique gaps as a violin plot
    • Displaying unique gaps as a box plot
  • Assess alignment quality via dotplots
    • Visualising an alignment with poor parameter choices
    • Visualising an alignment with good parameter choices
  • Dotplot with annotated sequences
    • Reloading from json
    • Removing annotation tracks
  • Dotplot basics
    • Modifying the matching parameters
    • Displaying dotplot for the reverse complement
    • Setting plot attributes
  • Coevolution analysis
    • Display coevolution as a heatmap
    • Display coevolution scores as a Violin plot
    • Display coevolution scores as a Boxplot
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Sequence Features

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Sequence logos

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Information analysis of an alignment

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Counting gaps per sequence

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Assess alignment quality via dotplots

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Dotplot with annotated sequences

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Dotplot basics

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Coevolution analysis

Phylogenetic Trees¶

  • Showing Bootstrap Support
    • Change the placement of support text
  • Square Dendrogram Style
    • Colouring a set of edges
    • With Contemporaneous Tips
  • Radial Dendrogram Style
    • With Contemporaneous Tips
  • Circular Dendrogram Style
    • Colouring a set of edges
    • With Contemporaneous Tips
  • Angular Dendrogram Style
    • With Contemporaneous Tips
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Showing Bootstrap Support

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Square Dendrogram Style

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Radial Dendrogram Style

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Circular Dendrogram Style

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Angular Dendrogram Style

© Copyright 2020-2024, cogent3 Team.

Created using Sphinx 7.2.6.