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cogent3 2025.03.24 documentation - Home cogent3 2025.03.24 documentation - Home
  • Image Gallery
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    • Project History
    • How does cogent3 relate to PyCogent?
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  • Image Gallery
  • Installation
  • User Guides
  • Community
  • License
  • Project History
  • How does cogent3 relate to PyCogent?
  • Projects using cogent3
  • Data Files Used in the Documentation
  • Index
  • GitHub

Section Navigation

  • Sequence Features
  • Sequence logos
  • Information analysis of an alignment
  • Counting gaps per sequence
  • Assess alignment quality via dotplots
  • Dotplot with annotated sequences
  • Dotplot basics
  • Coevolution analysis
  • Showing Bootstrap Support
  • Square Dendrogram Style
  • Radial Dendrogram Style
  • Circular Dendrogram Style
  • Angular Dendrogram Style
  • Image Gallery

Image Gallery#

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

Alignments & Sequences#

Sequence Features
Sequence logos
Information analysis of an alignment
Counting gaps per sequence
Assess alignment quality via dotplots
Dotplot with annotated sequences
Dotplot basics
Coevolution analysis

Phylogenetic Trees#

Showing Bootstrap Support
Square Dendrogram Style
Radial Dendrogram Style
Circular Dendrogram Style
Angular Dendrogram Style

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Making Sense from Sequence

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Sequence Features

On this page
  • Alignments & Sequences
  • Phylogenetic Trees

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