• 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

System requirements

The system requirements of the Phylogeny Module are:

• Windows XP, Windows Vista, or Windows 7, Windows Server 2003 or Windows Server 2008
• Mac OS X 10.6 or later. However, Mac OS X 10.5.8 is supported on 64-bit Intel systems.
• Linux: Red Hat 5.0 or later. SUSE 10.2 or later. Fedora 6 or later.
• 32 or 64 bit
• 1 GB RAM required
• 2 GB RAM recommended
• 1024 x 768 display recommended
• CLC Genomics Workbench