• Manuals

Browse the manual

• Introduction to the Phylogeny Module
  • Phylogeny
  • Features
• System requirements and installation of the Phylogeny Module
  • System requirements
  • How to install a plug-in
  • How to uninstall a plug-in
• Alignment of sequences
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • Join alignments
    • How alignments are joined
  • Pairwise comparison
    • Pairwise comparison on alignment selection
    • Pairwise comparison parameters
    • The pairwise comparison table
• Create Trees
  • K-mer Based Tree Construction
  • Create tree
  • Model Testing
  • Maximum Likelihood Phylogeny
  • Bioinformatics explained
    • Substitution models and distance estimation
    • K-mer based distance estimation
    • Distance based reconstruction methods
    • Maximum likelihood reconstruction methods
    • Bootstrap tests
• Tree Settings
  • Minimap
  • Tree layout
  • Node settings
  • Label settings
  • Background settings
  • Branch layout
  • Bootstrap settings
  • Metadata
  • Node right click menu
• Metadata and Phylogenetic Trees
  • Table Settings and Filtering
  • Add or modify metadata
  • Selection of specific nodes
• Bibliography

Introduction to the Phylogeny Module